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BibTex library of manually curated list of scientific papers reporting (or potentially) reporting Staphylococcus aureus genome sequencing. Please let me know ([email protected]) about missing articles.
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2018-03-20-Staph_genomes.bib
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@ARTICLE{Uhlemann2014-jn,
title = "Molecular tracing of the emergence, diversification, and
transmission of S. aureus sequence type 8 in a New York community",
author = "Uhlemann, Anne-Catrin and Dordel, Janina and Knox, Justin R and
Raven, Kathy E and Parkhill, Julian and Holden, Matthew T G and
Peacock, Sharon J and Lowy, Franklin D",
abstract = "During the last 2 decades, community-associated
methicillin-resistant Staphylococcus aureus (CA-MRSA) strains
have dramatically increased the global burden of S. aureus
infections. The pandemic sequence type (ST)8/pulsed-field gel
type USA300 is the dominant CA-MRSA clone in the United States,
but its evolutionary history and basis for biological success are
incompletely understood. Here, we use whole-genome sequencing of
387 ST8 isolates drawn from an epidemiological network of CA-MRSA
infections and colonizations in northern Manhattan to explore
short-term evolution and transmission patterns. Phylogenetic
analysis predicted that USA300 diverged from a most common recent
ancestor around 1993. We found evidence for multiple
introductions of USA300 and reconstructed the phylogeographic
spread of isolates across neighborhoods. Using pair-wise
single-nucleotide polymorphism distances as a measure of genetic
relatedness between isolates, we observed that most USA300
isolates had become endemic in households, indicating their
critical role as reservoirs for transmission and diversification.
Using the maximum single-nucleotide polymorphism variability of
isolates from within households as a threshold, we identified
several possible transmission networks beyond households. Our
study also revealed the evolution of a fluoroquinolone-resistant
subpopulation in the mid-1990s and its subsequent expansion at a
time of high-frequency outpatient antibiotic use. This
high-resolution phylogenetic analysis of ST8 has documented the
genomic changes associated with USA300 evolution and how some of
its recent evolution has been shaped by antibiotic use. By
integrating whole-genome sequencing with detailed epidemiological
analyses, our study provides an important framework for
delineating the full diversity and spread of USA300 and other
emerging pathogens in large urban community populations.",
journal = "Proc. Natl. Acad. Sci. U. S. A.",
month = apr,
year = 2014,
keywords = "Staphylococcus;evolution;colonization;Staph\_evolutionary\_history;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Boyle-Vavra2015-pc,
title = "{USA300} and {USA500} Clonal Lineages of Staphylococcus aureus
Do Not Produce a Capsular Polysaccharide Due to Conserved
Mutations in the cap5 Locus",
author = "Boyle-Vavra, Susan and Li, Xue and Alam, Md Tauqeer and Read,
Timothy D and Sieth, Julia and Cywes-Bentley, Colette and
Dobbins, Ginette and David, Michael Z and Kumar, Neha and Eells,
Samantha J and Miller, Loren G and Boxrud, David J and Chambers,
Henry F and Lynfield, Ruth and Lee, Jean C and Daum, Robert S",
abstract = "UNLABELLED: The surface capsular polysaccharide (CP) is a
virulence factor that has been used as an antigen in several
successful vaccines against bacterial pathogens. A vaccine has
not yet been licensed against Staphylococcus aureus, although
two multicomponent vaccines that contain CP antigens are in
clinical trials. In this study, we evaluated CP production in
USA300 methicillin-resistant S. aureus (MRSA) isolates that have
become the predominant community-associated MRSA clones in the
United States. We found that all 167 USA300 MRSA and 50 USA300
methicillin-susceptible S. aureus (MSSA) isolates were CP
negative (CP(-)). Moreover, all 16 USA500 isolates, which have
been postulated to be the progenitor lineage of USA300, were
also CP(-). Whole-genome sequence analysis of 146 CP(-) USA300
MRSA isolates revealed they all carry a cap5 locus with 4
conserved mutations compared with strain Newman. Genetic
complementation experiments revealed that three of these
mutations (in the cap5 promoter, cap5D nucleotide 994, and cap5E
nucleotide 223) ablated CP production in USA300 and that Cap5E75
Asp, located in the coenzyme-binding domain, is essential for
capsule production. All but three USA300 MSSA isolates had the
same four cap5 mutations found in USA300 MRSA isolates. Most
isolates with a USA500 pulsotype carried three of these four
USA300-specific mutations, suggesting the fourth mutation
occurred in the USA300 lineage. Phylogenetic analysis of the cap
loci of our USA300 isolates as well as publicly available
genomes from 41 other sequence types revealed that the
USA300-specific cap5 mutations arose sequentially in S. aureus
in a common ancestor of USA300 and USA500 isolates. IMPORTANCE:
The USA300 MRSA clone emerged as a community-associated pathogen
in the United States nearly 20 years ago. Since then, it has
rapidly disseminated and now causes health care-associated
infections. This study shows that the CP-negative (CP(-))
phenotype has persisted among USA300 isolates and is a universal
and characteristic trait of this highly successful MRSA lineage.
It is important to note that a vaccine consisting solely of CP
antigens would not likely demonstrate high efficacy in the U.S.
population, where about half of MRSA isolates comprise USA300.
Moreover, conversion of a USA300 strain to a CP-positive (CP(+))
phenotype is unlikely in vivo or in vitro since it would require
the reversion of 3 mutations. We have also established that
USA300 MSSA isolates and USA500 isolates are CP(-) and provide
new insight into the evolution of the USA300 and USA500
lineages.",
journal = "MBio",
publisher = "American Society for Microbiology",
volume = 6,
number = 2,
pages = "e02585--14",
month = apr,
year = 2015,
keywords = "Staphylococcus;My
Publications;My\_Peer\_reviewed;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers"
}
@ARTICLE{Alam2015-oc,
title = "Transmission and Microevolution of {USA300} {MRSA} in {U.S}.
Households: Evidence from {Whole-Genome} Sequencing",
author = "Alam, Md Tauqeer and Read, Timothy D and Petit, Robert A and
Boyle-Vavra, Susan and Miller, Loren G and Eells, Samantha J and
Daum, Robert S and David, Michael Z",
abstract = "UNLABELLED: Methicillin-resistant Staphylococcus aureus (MRSA)
USA300 is a successful S. aureus clone in the United States and
a common cause of skin and soft tissue infections (SSTIs). We
performed whole-genome sequencing (WGS) of 146 USA300 MRSA
isolates from SSTIs and colonization cultures obtained from an
investigation conducted from 2008 to 2010 in Chicago and Los
Angeles households that included an index case with an S. aureus
SSTI. Identifying unique single nucleotide polymorphisms (SNPs)
and analyzing whole-genome phylogeny, we characterized isolates
to understand transmission dynamics, genetic relatedness, and
microevolution of USA300 MRSA within the households. We also
compared the 146 USA300 MRSA isolates from our study with the
previously published genome sequences of the USA300 MRSA
isolates from San Diego (n = 35) and New York City (n = 277). We
found little genetic variation within the USA300 MRSA household
isolates from Los Angeles (mean number of SNPs $\pm$ standard
deviation, 17.6 $\pm$ 35; $\pi$ nucleotide diversity, 3.1
$\times$ 10(-5)) or from Chicago (mean number of SNPs $\pm$
standard deviation, 12 $\pm$ 19; $\pi$ nucleotide diversity, 3.1
$\times$ 10(-5)). The isolates within a household clustered into
closely related monophyletic groups, suggesting the introduction
into and transmission within each household of a single common
USA300 ancestral strain. From a Bayesian evolutionary
reconstruction, we inferred that USA300 persisted within
households for 2.33 to 8.35 years prior to sampling. We also
noted that fluoroquinolone-resistant USA300 clones emerged
around 1995 and were more widespread in Los Angeles and New York
City than in Chicago. Our findings strongly suggest that unique
USA300 MRSA isolates are transmitted within households that
contain an individual with an SSTI. Decolonization of household
members may be a critical component of prevention programs to
control USA300 MRSA spread in the United States. IMPORTANCE:
USA300, a virulent and easily transmissible strain of
methicillin-resistant Staphylococcus aureus (MRSA), is the
predominant community-associated MRSA clone in the United
States. It most commonly causes skin infections but also causes
necrotizing pneumonia and endocarditis. Strategies to limit the
spread of MRSA in the community can only be effective if we
understand the most common sources of transmission and the
microevolutionary processes that provide a fitness advantage to
MRSA. We performed a whole-genome sequence comparison of 146
USA300 MRSA isolates from Chicago and Los Angeles. We show that
households represent a frequent site of transmission and a
long-term reservoir of USA300 strains; individuals within
households transmit the same USA300 strain among themselves. Our
study also reveals that a large proportion of the USA300
isolates sequenced are resistant to fluoroquinolone antibiotics.
The significance of this study is that if households serve as
long-term reservoirs of USA300, household MRSA eradication
programs may result in a uniquely effective control method.",
journal = "MBio",
publisher = "American Society for Microbiology",
volume = 6,
number = 2,
pages = "e00054--15",
month = mar,
year = 2015,
keywords = "Staphylococcus;My Publications;bacterial comparative
genomics;antibiotcs-evolution-fitness;My\_Peer\_reviewed;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Glaser2016-qq,
title = "Demography and Intercontinental Spread of the {USA300}
{Community-Acquired} {Methicillin-Resistant} Staphylococcus
aureus Lineage",
author = "Glaser, Philippe and Martins-Sim{\~o}es, Patr{\'\i}cia and
Villain, Adrien and Barbier, Maxime and Tristan, Anne and
Bouchier, Christiane and Ma, Laurence and Bes, Michele and
Laurent, Frederic and Guillemot, Didier and Wirth, Thierry and
Vandenesch, Fran{\c c}ois",
abstract = "Community-acquired methicillin-resistant Staphylococcus aureus
(CA-MRSA) was recognized worldwide during the 1990s; in less than
a decade, several genetically distinct CA-MRSA lineages carrying
Panton-Valentine leukocidin genes have emerged on every
continent. Most notably, in the United States, the sequence type
18-IV (ST8-IV) clone known as USA300 has become highly prevalent,
outcompeting methicillin-susceptible S. aureus (MSSA) and other
MRSA strains in both community and hospital settings. CA-MRSA
bacteria are much less prevalent in Europe, where the European
ST80-IV European CA-MRSA clone, USA300 CA-MRSA strains, and other
lineages, such as ST22-IV, coexist. The question that arises is
whether the USA300 CA-MRSA present in Europe (i) was imported
once or on very few occasions, followed by a broad geographic
spread, anticipating an increased prevalence in the future, or
(ii) derived from multiple importations with limited spreading
success. In the present study, we applied whole-genome sequencing
to a collection of French USA300 CA-MRSA strains responsible for
sporadic cases and micro-outbreaks over the past decade and
United States ST8 MSSA and MRSA isolates. Genome-wide
phylogenetic analysis demonstrated that the population structure
of the French isolates is the product of multiple introductions
dating back to the onset of the USA300 CA-MRSA clone in North
America. Coalescent-based demography of the USA300 lineage shows
that a strong expansion occurred during the 1990s concomitant
with the acquisition of the arginine catabolic mobile element and
antibiotic resistance, followed by a sharp decline initiated
around 2008, reminiscent of the rise-and-fall pattern previously
observed in the ST80 lineage. A future expansion of the USA300
lineage in Europe is therefore very unlikely.IMPORTANCE To trace
the origin, evolution, and dissemination pattern of the USA300
CA-MRSA clone in France, we sequenced a collection of strains of
this lineage from cases reported in France in the last decade and
compared them with 431 ST8 strains from the United States. We
determined that the French CA-MRSA USA300 sporadic and
micro-outbreak isolates resulted from multiple independent
introductions of the USA300 North American lineage. At a global
level, in the transition from an MSSA lineage to a successful
CA-MRSA clone, it first became resistant to multiple antibiotics
and acquired the arginine catabolic mobile element and
subsequently acquired resistance to fluoroquinolones, and these
two steps were associated with a dramatic demographic expansion.
This expansion was followed by the current stabilization and
expected decline of this lineage. These findings highlight the
significance of horizontal gene acquisitions and point mutations
in the success of such disseminated clones and illustrate their
cyclic and sporadic life cycle.",
journal = "MBio",
volume = 7,
number = 1,
month = mar,
year = 2016,
keywords = "
Staphylococcus;evolution;demography;Staph\_evolutionary\_history;bacterial
comparative
genomics;Staph\_evolutionary\_history/USA300\_evolution;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Read-lab-shared;Papers\_for\_Michelle;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers"
}
@ARTICLE{Toleman2016-qd,
title = "Systematic surveillance detects multiple silent introductions and
household transmission of methicillin-resistant Staphylococcus
aureus {USA300} in the east of England",
author = "Toleman, Michelle S and Reuter, Sandra and Coll, Francesc and
Harrison, Ewan M and Blane, Beth and Brown, Nicholas M and
T{\"o}r{\"o}k, M Est{\'e}e and Parkhill, Julian and Peacock,
Sharon J",
abstract = "Background. The spread of USA300 methicillin-resistant
Staphylococcus aureus (MRSA) across the United States (US)
resulted in an epidemic of infections. In Europe, only sporadic
cases or small clusters of USA300 infections are described and
its prevalence in England is unknown. We conducted prospective
surveillance for USA300 in the east of England.Methods. We
undertook a 12-month prospective observational cohort study of
all individuals with MRSA isolated from community and hospital
samples submitted to a microbiology laboratory. At least one MRSA
isolate from each individual was whole-genome sequenced. USA300
was identified based on sequence analysis, and phylogenetic
comparisons were made between these and USA300 genomes from the
US.Results. Between April 2012-April 2013, we sequenced 2,283
MRSA isolates (carriage screens and clinical samples) from 1,465
individuals. USA300 was isolated from 24 (1.6\%) cases. Ten cases
(42\%) had skin and soft tissue infection and two cases had
invasive disease. Phylogenetic analyses identified multiple
introductions and household transmission of USA300.Conclusions.
Use of a diagnostic laboratory as a sentinel for surveillance has
identified repeated introductions of USA300 into the east of
England in 2012-2013, with evidence for limited transmission. Our
results show how systematic surveillance could provide an
early-warning of strain emergence and dissemination.",
journal = "J. Infect. Dis.",
month = apr,
year = 2016,
keywords = "Staphylococcus;bacterial comparative
genomics;Staph\_evolutionary\_history;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Ge2017-du,
title = "{MRSA} and multidrug-resistant Staphylococcus aureus in {U.S}.
retail meats, 2010-2011",
author = "Ge, Beilei and Mukherjee, Sampa and Hsu, Chih-Hao and Davis,
Johnnie A and Tran, Thu Thuy T and Yang, Qianru and Abbott, Jason
W and Ayers, Sherry L and Young, Shenia R and Crarey, Emily T and
Womack, Niketta A and Zhao, Shaohua and McDermott, Patrick F",
abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) has been
detected in retail meats, although large-scale studies are
scarce. We conducted a one-year survey in 2010-2011 within the
framework of the National Antimicrobial Resistance Monitoring
System. Among 3520 retail meats collected from eight U.S. states,
982 (27.9\%) contained S. aureus and 66 (1.9\%) were positive for
MRSA. Approximately 10.4\% (107/1032) of S. aureus isolates,
including 37.2\% (29/78) of MRSA, were multidrug-resistant
(MDRSA). Turkey had the highest MRSA prevalence (3.5\%), followed
by pork (1.9\%), beef (1.7\%), and chicken (0.3\%). Whole-genome
sequencing was performed for all 66 non-redundant MRSA. Among
five multilocus sequence types identified, ST8 (72.7\%) and ST5
(22.7\%) were most common and livestock-associated MRSA ST398 was
assigned to one pork isolate. Eleven spa types were represented,
predominately t008 (43.9\%) and t2031 (22.7\%). All four types of
meats harbored t008, whereas t2031 was recovered from turkey
only. The majority of MRSA (84.8\%) possessed SCCmec IV and
62.1\% harbored Panton-Valentine leukocidin. Pulsed-field gel
electrophoresis showed that all ST8 MRSA belonged to the
predominant human epidemic clone USA300, and others included
USA100 and USA200. We conclude that a diverse MRSA population was
present in U.S. retail meats, albeit at low prevalence.",
journal = "Food Microbiol.",
volume = 62,
pages = "289--297",
month = apr,
year = 2017,
keywords = "LA-MRSA; MDRSA; MRSA; Retail meat; ST398;
USA300;Staphylococcus;colonization;Staph\_evolutionary\_history;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Popovich2017-mo,
title = "Genomic and Epidemiological Evidence for Community Origins of
{Hospital-Onset} {Methicillin-Resistant} Staphylococcus aureus
Bloodstream Infections",
author = "Popovich, Kyle J and Snitkin, Evan S and Hota, Bala and Green,
Stefan J and Pirani, Ali and Aroutcheva, Alla and Weinstein,
Robert A",
abstract = "Background.: We examined whether disparities existed in
hospital-onset (HO) Staphylococcus aureus bloodstream infections
(BSIs) and used whole-genome sequencing (WGS) to identify factors
associated with USA300 transmission networks. Methods.: We
evaluated HO methicillin-susceptible S. aureus (MSSA) and HO
methicillin-resistant S. aureus (MRSA) BSIs for 2009-2013 at 2
hospitals and used an adjusted incidence for modeling. WGS and
phylogenetic analyses were performed on a sample of USA300 BSI
isolates. Epidemiologic data were analyzed in the context of
phylogenetic reconstructions. Results.: On multivariate analysis,
male sex, African-American race, and non-Hispanic white
race/ethnicity were significantly associated with HO-MRSA BSIs
whereas Hispanic ethnicity was negatively associated (rate ratio,
0.41; P = .002). Intermixing of community-onset and HO-USA300
strains on the phylogenetic tree indicates that these strains
derive from a common pool. African-American race was the only
factor associated with genomic clustering of isolates.
Conclusions.: In a multicenter assessment of HO-S. aureus BSIs,
African-American race was significantly associated with HO-MRSA
but not MSSA BSIs. There appears to be a nexus of USA300
community and hospital transmission networks, with a community
factor being the primary driver. Our data suggest that HO-USA300
BSIs likely are due to colonizing strains acquired in the
community before hospitalization. Therefore, prevention efforts
may need to extend to the community for maximal benefit.",
journal = "J. Infect. Dis.",
month = may,
year = 2017,
keywords = "MRSA; Whole genome sequencing; bacteremia.;
disparities;Staphylococcus;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Planet2016-jd,
title = "Global Spread of the {Community-Associated}
{Methicillin-Resistant} Staphylococcus aureus {USA300} Latin
American Variant",
author = "Planet, Paul J and Diaz, Lorena and Rios, Rafael and Arias,
Cesar A",
journal = "J. Infect. Dis.",
volume = 214,
number = 10,
pages = "1609--1610",
month = nov,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN",
language = "en",
original_id = "379c0306-8718-0c37-9696-1b028a15d914"
}
@ARTICLE{Popovich2016-nk,
title = "Genomic Epidemiology of {USA300} {Methicillin-Resistant}
Staphylococcus aureus in an Urban Community",
author = "Popovich, Kyle J and Snitkin, Evan and Green, Stefan J and
Aroutcheva, Alla and Hayden, Mary K and Hota, Bala and Weinstein,
Robert A",
abstract = "BACKGROUND: In a community, it is unknown what factors account
for transmission of methicillin-resistant Staphylococcus aureus
(MRSA). We integrated whole genome sequencing (WGS) and
epidemiologic data to identify factors associated with MRSA
transmission networks in an urban community. METHODS: WGS was
performed on colonizing USA300 MRSA isolates from 74 individuals
within 72 hours of admission to a public hospital in Chicago, IL.
Single nucleotide variants (SNVs) were used to reconstruct the
phylogeny of sequenced isolates, and epidemiologic data was
overlaid to identify factors associated with transmission
networks. RESULTS: The maximum within-patient SNV difference for
an individual with multisite colonization was 41 SNVs, with no
systematic divergence among body sites. We observed a minimum of
7 SNVs and maximum of 153 SNVs between isolates from different
individuals. We identified 4 pairs of individuals whose isolates
were within 40 SNVs of each other. Putting our isolates in the
context of previously sequenced USA300 isolates from other
communities, we identified a 13-member group and two 4-member
groups that represent samples from putative local transmission
networks. Individuals in these groups were more likely to be
African American, to be human immunodeficiency virus-infected, to
reside in high detainee release areas, and to be current users of
illicit drugs. CONCLUSIONS: Using WGS, we observed potential
transmission networks in an urban community and that certain
epidemiologic factors were associated with inclusion in these
networks. Future work with contact tracing and advanced molecular
diagnostics may allow for identification of MRSA ``epicenters''
in the community where interventions can be targeted.",
journal = "Clin. Infect. Dis.",
volume = 62,
number = 1,
pages = "37--44",
month = jan,
year = 2016,
keywords = "MRSA; whole genome
sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Connolly2017-su,
title = "The identification of Staphylococcus aureus factors required for
pathogenicity and growth in human blood",
author = "Connolly, John and Boldock, Emma and Prince, Lynne R and Renshaw,
Stephen A and Whyte, Moira K and Foster, Simon J",
abstract = "Staphylococcus aureus is a human commensal but also has
devastating potential as an opportunist pathogen. S. aureus
bacteraemia is often associated with an adverse outcome. To
identify potential targets for novel control approaches we have
identified S. aureus components that are required for growth on
human blood. An ordered transposon mutant library was screened,
identifying 9 genes involved specifically in haemolysis or growth
on human blood agar compared to the parental strain. Three genes
(purA, purB and pabA) were subsequently found to be required for
pathogenesis in the zebrafish embryo infection model. The pabA
growth defect was specific to the red blood cell component of
human blood, showing no growth difference compared to the
parental strain on human serum, human plasma, sheep or horse
blood. PabA is required in the tetrahydrofolate (THF)
biosynthesis pathway. The pabA growth defect was found to be due
to a combination of loss of THF-dependent dTMP production by the
enzyme ThyA and an increased demand for pyrimidines in human
blood. Our work highlights pabA and the pyrimidine salvage
pathway as potential targets for novel therapeutics and suggests
a previously undefined role for a human blood factor in the
activity of sulphonamide antibiotics.",
journal = "Infect. Immun.",
month = aug,
year = 2017,
keywords = "Staphylococcus;bacerial\_genetics;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Read-lab-shared",
language = "en"
}
@ARTICLE{Von_Dach2016-wg,
title = "Comparative Genomics of {Community-Associated}
{Methicillin-Resistant} Staphylococcus aureus Shows the Emergence
of Clone {ST8-USA300} in Geneva, Switzerland",
author = "Von Dach, Elodie and Diene, Seydina M and Fankhauser, Carolina
and Schrenzel, Jacques and Harbarth, Stephan and Fran{\c c}ois,
Patrice",
abstract = "BACKGROUND: Previous investigations of community-associated
methicillin-resistant Staphylococcus aureus(CA-MRSA) isolates
have revealed a wide diversity of genetic backgrounds, with only
sporadic occurrence of ST8-USA300, in Geneva, Switzerland. We
conducted a molecular epidemiologic analysis to identify the
origin of a sudden increase of ST8 PVL-positive isolates in
Geneva during 2013. METHODS: On the basis of prospective CA-MRSA
surveillance, we collected colonizing and infecting ST8-USA300
isolates and compared them to non-ST8 CA-MRSA isolates.
Whole-genome sequencing (WGS) was performed for each isolate of
this collection, and discriminating molecular features were
linked to patient data. RESULTS: In 2013, 22 isolates with the
ST8-USA300 profile were identified among 46 cases of CA-MRSA. WGS
revealed 2 groups of strains that differed by the type of the
SCCmec IV element encoded and whether they harbored an arginine
catabolism mobile element (ACME) locus. ACME-negative strains
were mainly isolated from patients traveling in or originating
from South America. Single-nucleotide polymorphism positions in
isolate groups were used to infer their common ancestor,
determine their geographical origin, and trace their relatedness.
CONCLUSIONS: WGS allowed the identification of transmission
events and revealed that the increased prevalence of USA300
CA-MRSA isolates resulted from multiple importation events from
the Americas but not from local clonal expansion of a successful
clone.",
journal = "J. Infect. Dis.",
volume = 213,
number = 9,
pages = "1370--1379",
month = may,
year = 2016,
keywords = "USA300; comparative genomics; epidemiological survey; genome
evolution; high throughput sequencing; importation event;
methicillin-resistant Staphylococcus
aureus;Staphylococcus;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN",
language = "en"
}
% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Jamrozy2016-vu,
title = "Pan-genomic perspective on the evolution of the Staphylococcus
aureus {USA300} epidemic",
author = "Jamrozy, Dorota M and Harris, Simon R and Mohamed, Naglaa and
Peacock, Sharon J and Tan, Charles Y and Parkhill, Julian and
Anderson, Annaliesa S and Holden, Matthew T G",
abstract = "Staphylococcus aureus USA300 represents the dominant
community-associated methicillin-resistant S. aureus lineage in
the USA, where it is a major cause of skin and soft tissue
infections. Previous comparative genomic studies have described
the population structure and evolution of USA300 based on
geographically restricted isolate collections. Here, we
investigated the USA300 population by sequencing genomes of a
geographically distributed panel of 191 clinical S. aureus
isolates belonging to clonal complex 8 (CC8), derived from the
Tigecycline Evaluation and Surveillance Trial program. Isolates
were collected at 12 healthcare centres across nine USA states
in 2004, 2009 or 2010. Reconstruction of evolutionary
relationships revealed that CC8 was dominated by USA300 isolates
(154/191, 81 \%), which were heterogeneous and demonstrated
limited phylogeographic clustering. Analysis of the USA300 core
genomes revealed an increase in median pairwise SNP distance
from 62 to 98 between 2004 and 2010, with a stable pattern of
above average dN/dS ratios. The phylogeny of the USA300
population indicated that early diversification events led to
the formation of nested clades, which arose through cumulative
acquisition of predominantly non-synonymous SNPs in various
coding sequences. The accessory genome of USA300 was largely
homogenous and consisted of elements previously associated with
this lineage. We observed an emergence of SCCmec negative and
ACME negative USA300 isolates amongst more recent samples, and
an increase in the prevalence of ϕSa5 prophage. Together, the
analysed S. aureus USA300 collection revealed an evolving
pan-genome through increased core genome heterogeneity and
temporal variation in the frequency of certain accessory
elements.",
journal = "Microb Genom",
publisher = "Microbiology Society",
volume = 2,
number = 5,
pages = "e000058",
month = may,
year = 2016,
keywords = "Evolution; MRSA;
USA300;Staphylococcus;pangenome;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers",
language = "en"
}
% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Straus2017-ku,
title = "Origin, evolution, and global transmission of community-acquired
Staphylococcus aureus {ST8}",
author = "Strau{\ss}, Lena and Stegger, Marc and Akpaka, Patrick Eberechi
and Alabi, Abraham and Breurec, Sebastien and Coombs, Geoffrey
and Egyir, Beverly and Larsen, Anders Rhod and Laurent, Frederic
and Monecke, Stefan and Peters, Georg and Skov, Robert and
Strommenger, Birgit and Vandenesch, Fran{\c c}ois and Schaumburg,
Frieder and Mellmann, Alexander",
abstract = "USA300 is a pandemic clonal lineage of hypervirulent,
community-acquired, methicillin-resistant Staphylococcus aureus
(CA-MRSA) with specific molecular characteristics. Despite its
high clinical relevance, the evolutionary origin of USA300
remained unclear. We used comparative genomics of 224 temporal
and spatial diverse S. aureus isolates of multilocus sequence
type (ST) 8 to reconstruct the molecular evolution and global
dissemination of ST8, including USA300. Analyses of core SNP
diversity and accessory genome variations showed that the
ancestor of all ST8 S. aureus most likely emerged in Central
Europe in the mid-19th century. From here, ST8 was exported to
North America in the early 20th century and progressively
acquired the USA300 characteristics Panton-Valentine leukocidin
(PVL), SCCmec IVa, the arginine catabolic mobile element (ACME),
and a specific mutation in capsular polysaccharide gene cap5E
Although the PVL-encoding phage ϕSa2USA was introduced into the
ST8 background only once, various SCCmec types were introduced to
ST8 at different times and places. Starting from North America,
USA300 spread globally, including Africa. African USA300 isolates
have aberrant spa-types (t112, t121) and form a monophyletic
group within the clade of North American USA300. Large parts of
ST8 methicillin-susceptible S. aureus (MSSA) isolated in Africa
represent a symplesiomorphic group of ST8 (i.e., a group
representing the characteristics of the ancestor), which are
rarely found in other world regions. Isolates previously
discussed as USA300 ancestors, including USA500 and a
``historic'' CA-MRSA from Western Australia, were shown to be
only distantly related to recent USA300 clones.",
journal = "Proc. Natl. Acad. Sci. U. S. A.",
month = nov,
year = 2017,
keywords = "Africa; CA-MRSA; USA300; comparative genomics; molecular
evolution;Staphylococcus;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Spoor2013-nc,
title = "Livestock Origin for a Human Pandemic Clone of
{Community-Associated} {Methicillin-Resistant} Staphylococcus
aureus",
author = "Spoor, L E and Mcadam, P R and Weinert, L A and Rambaut, A and
Hasman, H and Aarestrup, F M and Kearns, A M and Larsen, A R and
Skov, R L and Fitzgerald, J R",
journal = "MBio",
volume = 4,
number = 4,
pages = "e00356--13--e00356--13",
year = 2013,
keywords = "Staphylococcus;imported\_from\_papers\_14Nov2013;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
}
@ARTICLE{Kos2012-xa,
title = "Comparative Genomics of {Vancomycin-Resistant} Staphylococcus
aureus Strains and Their Positions within the Clade Most Commonly
Associated with {Methicillin-Resistant} S. aureus
{Hospital-Acquired} Infection in the United States",
author = "Kos, V N and Desjardins, C A and Griggs, A and Cerqueira, G and
Van Tonder, A and Holden, M T G and Godfrey, P and Palmer, K L
and Bodi, K and Mongodin, E F and Wortman, J and Feldgarden, M
and Lawley, T and Gill, S R and Haas, B J and Birren, B and
Gilmore, M S",
abstract = "ABSTRACT Staphylococcus aureus is a human commensal bacterium and
a prominent cause of infections globally. The high incidence of
S. aureus infections is compounded by the ability of the microbe
to readily acquire resistance to antibiotics. In the United
States, methicillin-resistant S. aureus (MRSA) is a leading cause
of morbidity and mortality by a single infectious agent.
Therapeutic options for severe MRSA infections are limited to a
few antibiotics to which the organism is typically susceptible,
including vancomycin. Acquisition of high-level vancomycin
resistance by MRSA is a major concern, but to date, there have
been only 12 vancomycin-resistant S. aureus (VRSA) isolates
reported in the United States and all belong to a phylogenetic
lineage known as clonal complex 5. To gain enhanced understanding
of the genetic characteristics conducive to the acquisition of
vancomycin resistance by S. aureus, V. N. Kos et al. performed
whole-genome sequencing of all 12 VRSA isolates and compared the
DNA sequences to the genomes of other S. aureus strains. The
findings provide new information about the evolutionary history
of VRSA and identify genetic features that may bear on the
relationship between S. aureus clonal complex 5 strains and the
acquisition of vancomycin resistance genes from enterococci.",
journal = "MBio",
volume = 3,
number = 3,
pages = "e00112--12--e00112--12",
year = 2012,
keywords = "
antibiotics;Staphylococcus;imported\_from\_papers\_14Nov2013;bacterial
comparative genomics;Teaching antibiotic resistance
genomics;R-M;Staph\_evolutionary\_history;antibiotcs-evolution-fitness;MRSA-VRSA-gene\_transfer;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Lowder2009-jk,
title = "Recent human-to-poultry host jump, adaptation, and pandemic
spread of Staphylococcus aureus",
author = "Lowder, V, Bethan and Guinane, Caitriona M and Ben Zakour, Nouri
L and Weinert, Lucy A and Conway-Morris, Andrew and Cartwright,
Robyn A and Simpson, A John and Rambaut, Andrew and N{\"u}bel,
Ulrich and Fitzgerald, J Ross",
abstract = "The impact of globalization on the emergence and spread of
pathogens is an important veterinary and public health issue.
Staphylococcus aureus is a notorious human pathogen associated
with serious nosocomial and community-acquired infections. In
addition, S. aureus is a major cause of animal diseases including
skeletal infections of poultry, which are a large economic burden
on the global broiler chicken industry. Here, we provide evidence
that the majority of S. aureus isolates from broiler chickens are
the descendants of a single human-to-poultry host jump that
occurred approximately 38 years ago (range, 30 to 63 years ago)
by a subtype of the worldwide human ST5 clonal lineage unique to
Poland. In contrast to human subtypes of the ST5 radiation, which
demonstrate strong geographic clustering, the poultry ST5 clade
was distributed in different continents, consistent with wide
dissemination via the global poultry industry distribution
network. The poultry ST5 clade has undergone genetic
diversification from its human progenitor strain by acquisition
of novel mobile genetic elements from an avian-specific accessory
gene pool, and by the inactivation of several proteins important
for human disease pathogenesis. These genetic events have
resulted in enhanced resistance to killing by chicken
heterophils, reflecting avian host-adaptive evolution. Taken
together, we have determined the evolutionary history of a major
new animal pathogen that has undergone rapid avian host
adaptation and intercontinental dissemination. These data provide
a new paradigm for the impact of human activities on the
emergence of animal pathogens.",
journal = "Proc. Natl. Acad. Sci. U. S. A.",
volume = 106,
number = 46,
pages = "19545--19550",
year = 2009,
keywords = "Staphylococcus;imported\_from\_papers\_14Nov2013;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
}
@ARTICLE{Harris2010-uv,
title = "Evolution of {MRSA} During Hospital Transmission and
Intercontinental Spread",
author = "Harris, S R and Feil, E J and Holden, M T G and Quail, M A and
Nickerson, E K and Chantratita, N and Gardete, S and Tavares, A
and Day, N and Lindsay, J A and Edgeworth, J D and de Lencastre,
H and Parkhill, J and Peacock, S J and Bentley, S D",
abstract = "Current methods for differentiating isolates of predominant
lineages of pathogenic bacteria often do not provide sufficient
resolution to define precise relationships. Here, we describe a
high-throughput genomics approach that provides a high-resolution
view of the epidemiology and microevolution of a dominant strain
of methicillin-resistant Staphylococcus aureus (MRSA). This
approach reveals the global geographic structure within the
lineage, its intercontinental transmission through four decades,
and the potential to trace person-to-person transmission within a
hospital environment. The ability to interrogate and resolve
bacterial populations is applicable to a range of infectious
diseases, as well as microbial ecology.",
journal = "Science",
volume = 327,
number = 5964,
pages = "469--474",
year = 2010,
keywords = "Staphylococcus;imported\_from\_papers\_14Nov2013;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Howden2010-ek,
title = "Complete genome sequence of Staphylococcus aureus strain
{JKD6008}, an {ST239} clone of methicillin-resistant
Staphylococcus aureus with intermediate-level vancomycin
resistance",
author = "Howden, Benjamin P and Seemann, Torsten and Harrison, Paul F and
McEvoy, Chris R and Stanton, Jo-Ann L and Rand, Christy J and
Mason, Chris W and Jensen, Slade O and Firth, Neville and Davies,
John K and Johnson, Paul D R and Stinear, Timothy P",
abstract = "We report here the complete 2.92-Mb genome sequence of a clinical
isolate of methicillin-resistant Staphylococcus aureus subsp.
aureus that demonstrates intermediate-level vancomycin
resistance. The strain, named JKD6008, belongs to multilocus
sequence type 239 and was isolated from the bloodstream of a
patient in New Zealand in 2003.",
journal = "J. Bacteriol.",
volume = 192,
number = 21,
pages = "5848--5849",
year = 2010,
keywords = "Staphylococcus;imported\_from\_papers\_14Nov2013;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Gao2010-fv,
title = "Two novel point mutations in clinical Staphylococcus aureus
reduce linezolid susceptibility and switch on the stringent
response to promote persistent infection",
author = "Gao, Wei and Chua, Kyra and Davies, John K and Newton, Hayley J
and Seemann, Torsten and Harrison, Paul F and Holmes, Natasha E
and Rhee, Hyun-Woo and Hong, Jong-In and Hartland, Elizabeth L
and Stinear, Timothy P and Howden, Benjamin P",
abstract = "Staphylococcus aureus frequently invades the human bloodstream,
leading to life threatening bacteremia and often secondary foci
of infection. Failure of antibiotic therapy to eradicate
infection is frequently described; in some cases associated with
altered S. aureus antimicrobial resistance or the small colony
variant (SCV) phenotype. Newer antimicrobials, such as
linezolid, remain the last available therapy for some patients
with multi-resistant S. aureus infections. Using comparative and
functional genomics we investigated the molecular determinants
of resistance and SCV formation in sequential S. aureus isolates
from a patient who had a persistent and recurrent S. aureus
infection, after failed therapy with multiple antimicrobials,
including linezolid. Two point mutations in key staphylococcal
genes dramatically affected clinical behaviour of the bacterium,
altering virulence and antimicrobial resistance. Most
strikingly, a single nucleotide substitution in relA (SACOL1689)
reduced RelA hydrolase activity and caused accumulation of the
intracellular signalling molecule guanosine 3',
5'-bis(diphosphate) (ppGpp) and permanent activation of the
stringent response, which has not previously been reported in S.
aureus. Using the clinical isolate and a defined mutant with an
identical relA mutation, we demonstrate for the first time the
impact of an active stringent response in S. aureus, which was
associated with reduced growth, and attenuated virulence in the
Galleria mellonella model. In addition, a mutation in rlmN
(SACOL1230), encoding a ribosomal methyltransferase that
methylates 23S rRNA at position A2503, caused a reduction in
linezolid susceptibility. These results reinforce the exquisite
adaptability of S. aureus and show how subtle molecular changes
cause major alterations in bacterial behaviour, as well as
highlighting potential weaknesses of current antibiotic
treatment regimens.",
journal = "PLoS Pathog.",
publisher = "Public Library of Science",
volume = 6,
number = 6,
pages = "e1000944",
year = 2010,
keywords = "Staphylococcus;imported\_from\_papers\_14Nov2013;bacterial
comparative genomics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Young2012-vu,
title = "Evolutionary dynamics of Staphylococcus aureus during progression
from carriage to disease",
author = "Young, Bernadette C and Golubchik, Tanya and Batty, Elizabeth M
and Fung, Rowena and Larner-Svensson, Hanna and Votintseva,
Antonina A and Miller, Ruth R and Godwin, Heather and Knox, Kyle
and Everitt, Richard G and Iqbal, Zamin and Rimmer, Andrew J and
Cule, Madeleine and Ip, Camilla L C and Didelot, Xavier and
Harding, Rosalind M and Donnelly, Peter and Peto, Tim E and
Crook, Derrick W and Bowden, Rory and Wilson, Daniel J",
abstract = "Whole-genome sequencing offers new insights into the evolution of
bacterial pathogens and the etiology of bacterial disease.
Staphylococcus aureus is a major cause of bacteria-associated
mortality and invasive disease and is carried asymptomatically by
27\% of adults. Eighty percent of bacteremias match the carried
strain. However, the role of evolutionary change in the pathogen
during the progression from carriage to disease is incompletely
understood. Here we use high-throughput genome sequencing to
discover the genetic changes that accompany the transition from
nasal carriage to fatal bloodstream infection in an individual
colonized with methicillin-sensitive S. aureus. We found a
single, cohesive population exhibiting a repertoire of 30
single-nucleotide polymorphisms and four insertion/deletion
variants. Mutations accumulated at a steady rate over a 13-mo
period, except for a cluster of mutations preceding the
transition to disease. Although bloodstream bacteria differed by
just eight mutations from the original nasally carried bacteria,
half of those mutations caused truncation of proteins, including
a premature stop codon in an AraC-family transcriptional
regulator that has been implicated in pathogenicity. Comparison
with evolution in two asymptomatic carriers supported the
conclusion that clusters of protein-truncating mutations are
highly unusual. Our results demonstrate that bacterial diversity
in vivo is limited but nonetheless detectable by whole-genome
sequencing, enabling the study of evolutionary dynamics within
the host. Regulatory or structural changes that occur during
carriage may be functionally important for pathogenesis;
therefore identifying those changes is a crucial step in
understanding the biological causes of invasive bacterial
disease.",
journal = "Proceedings of the National Academy of Sciences",
volume = 109,
number = 12,
pages = "4550--4555",
year = 2012,
keywords = "Staphylococcus;colonization;imported\_from\_papers\_14Nov2013;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Kser2012-yi,
title = "Rapid whole-genome sequencing for investigation of a neonatal
{MRSA} outbreak",
author = "K{\"o}ser, Claudio U and Holden, Matthew T G and Ellington,
Matthew J and Cartwright, Edward J P and Brown, Nicholas M and
Ogilvy-Stuart, Amanda L and Hsu, Li Yang and Chewapreecha, Claire
and Croucher, Nicholas J and Harris, Simon R and Sanders, Mandy
and Enright, Mark C and Dougan, Gordon and Bentley, Stephen D and
Parkhill, Julian and Fraser, Louise J and Betley, Jason R and
Schulz-Trieglaff, Ole B and Smith, Geoffrey P and Peacock, Sharon
J",
abstract = "BACKGROUND:Isolates of methicillin-resistant Staphylococcus
aureus (MRSA) belonging to a single lineage are often
indistinguishable by means of current typing techniques.
Whole-genome sequencing may provide improved resolution to define
transmission pathways and characterize outbreaks.METHODS:We
investigated a putative MRSA outbreak in a neonatal intensive
care unit. By using rapid high-throughput sequencing technology
with a clinically relevant turnaround time, we retrospectively
sequenced the DNA from seven isolates associated with the
outbreak and another seven MRSA isolates associated with carriage
of MRSA or bacteremia in the same hospital.RESULTS:We constructed
a phylogenetic tree by comparing single-nucleotide polymorphisms
(SNPs) in the core genome to a reference genome (an epidemic MRSA
clone, EMRSA-15 [sequence type 22]). This revealed a distinct
cluster of outbreak isolates and clear separation between these
and the nonoutbreak isolates. A previously missed transmission
event was detected between two patients with bacteremia who were
not part of the outbreak. We created an artificial ``resistome''
of antibiotic-resistance genes and demonstrated concordance
between it and the results of phenotypic susceptibility testing;
we also created a ``toxome'' consisting of toxin genes. One
outbreak isolate had a hypermutator phenotype with a higher
number of SNPs than the other outbreak isolates, highlighting the
difficulty of imposing a simple threshold for the number of SNPs
between isolates to decide whether they are part of a recent
transmission chain.CONCLUSIONS:Whole-genome sequencing can
provide clinically relevant data within a time frame that can
influence patient care. The need for automated data
interpretation and the provision of clinically meaningful reports
represent hurdles to clinical implementation. (Funded by the U.K.
Clinical Research Collaboration Translational Infection Research
Initiative and others.).",
journal = "N. Engl. J. Med.",
volume = 366,
number = 24,
pages = "2267--2275",
year = 2012,
keywords = "Staphylococcus;imported\_from\_papers\_14Nov2013;Teaching
antibiotic resistance
genomics;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Kant2015-wt,
title = "Genome Sequences of Four Staphylococcus aureus Strains Isolated
from Bovine Mastitis",
author = "Kant, Ravi and Taponen, Suvi and Koort, Joanna and Paulin, Lars
and {\AA}vall-J{\"a}{\"a}skel{\"a}inen, Silja and Palva, Airi",
abstract = "Staphylococcus aureus is a major causative agent of mastitis in
dairy cows. The pathogenicity of S. aureus may vary; it is able
to cause severe clinical mastitis, but most often it is
associated with chronic subclinical mastitis. Here, we present
the genome assemblies of four S. aureus strains from bovine
mastitis.",
journal = "Genome Announc.",
volume = 3,
number = 2,
month = apr,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Findley2014-rn,
title = "The skin microbiome: a focus on pathogens and their association
with skin disease",
author = "Findley, Keisha and Grice, Elizabeth A",
journal = "PLoS Pathog.",
volume = 10,
number = 10,
pages = "e1004436",
month = oct,
year = 2014,
keywords = "microbiome;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Jia2015-ri,
title = "Characterization and complete genome sequence analysis of
Staphylococcus aureus bacteriophage {JS01}",
author = "Jia, Hongying and Dong, Wenyang and Yuan, Lvfeng and Ma, Jiale
and Bai, Qinqin and Pan, Zihao and Lu, Chengping and Yao, Huochun",
abstract = "Staphylococcus aureus is a primary pathogen that causes bovine
mastitis resulting in serious economic losses and herd management
problems in dairy cows. A novel bacteriophage, JS01, specifically
infecting bovine S. aureus, was isolated from milk of
mastitis-affected cattle. TEM observation showed that it belonged
to the family Siphovirus. The JS01 strain demonstrated a broad
host range. The prediction result of PHACTS suggested that the
JS01 strain was temperate phage. The JS01 genome is 43,458 bp
long, with a GC content of 33.32\% and no tRNAs. Annotation and
functional analysis of the predicted ORFs revealed six functional
groups: structure and morphology, DNA replication and regulation,
packaging, lysogeny, lysis, and pathogenicity. Comparative
analysis between JS01, S. aureus MSSA476, and S. aureus prophage
PVL was also performed. The characterization and genomic analysis
of JS01 provide a better understanding of S. aureus-targeting
bacteriophages and useful information for the development of
phage-based biocontrol agents against S. aureus.",
journal = "Virus Genes",
volume = 50,
number = 2,
pages = "345--348",
month = apr,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Zhang2014-eo,
title = "Complete Genome Sequence of Staphylococcus aureus {XN108}, an
{ST239-MRSA-SCCmec} {III} Strain with Intermediate Vancomycin
Resistance Isolated in Mainland China",
author = "Zhang, Xia and Xu, Xiaomeng and Yuan, Wenchang and Hu, Qiwen and
Shang, Weilong and Hu, Xiaomei and Tong, Yigang and Rao, Xiancai",
abstract = "ST239-MRSA-SCCmec III (ST239, sequence type 239; MRSA,
methicillin-resistant Staphylococcus aureus; SCCmec III,
staphylococcal cassette chromosome mec type III) is the most
predominant clone of hospital-acquired methicillin-resistant S.
aureus in mainland China. We report here the complete genome
sequence of XN108, the first vancomycin-intermediate S. aureus
strain isolated from a steam-burned patient with a wound
infection.",
journal = "Genome Announc.",
volume = 2,
number = 4,
month = jul,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Suhaili2014-nb,
title = "Draft Genome Sequence of {Methicillin-Resistant} Staphylococcus
aureus {KT/Y21}, a Sequence Type 772 ({ST772}) Strain Isolated
from a Pediatric Blood Sample in Terengganu, Malaysia",
author = "Suhaili, Zarizal and Lean, Soo-Sum and Yahya, Azifah and Mohd
Desa, Mohd Nasir and Ali, Abdul Manaf and Yeo, Chew Chieng",
abstract = "Here, we report the draft genome sequence of a
methicillin-resistant Staphylococcus aureus (MRSA) strain,
KT/Y21, isolated from a blood sample of a pediatric patient. This
strain belongs to sequence type 772 (ST772), harbors the
staphylococcal cassette chromosome mec element (SCCmec) type V,
and is positive for the Panton-Valentine leukocidin (PVL)
pathogenic determinant.",
journal = "Genome Announc.",
volume = 2,
number = 2,
month = apr,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Swift2014-si,
title = "Complete Genome Sequence of Staphylococcus aureus Phage {GRCS}",
author = "Swift, Steven M and Nelson, Daniel C",
abstract = "The Staphylococcus aureus phage GRCS was isolated from a sewage
treatment facility in India and has shown potential for phage
therapy in a mouse model of bacteremia. Here, we report the
complete genome sequence of this bacteriophage.",
journal = "Genome Announc.",
volume = 2,
number = 2,
month = apr,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Hernandez2014-ft,
title = "Genome Sequences of Sequence Type 45 ({ST45}) Persistent
{Methicillin-Resistant} Staphylococcus aureus ({MRSA}) Bacteremia
Strain 300-169 and {ST45} Resolving {MRSA} Bacteremia Strain
301-188",
author = "Hernandez, David and Seidl, Kati and Corvaglia, Anna-Rita and
Bayer, Arnold S and Xiong, Yan Q and Fran{\c c}ois, Patrice",
abstract = "Persistent methicillin-resistant Staphylococcus aureus (MRSA)
bacteremia (positive blood cultures after $\geq$7 days)
represents a challenging subset of invasive MRSA infections. The
comparison of genome sequences of persistent (300-169) and
resolving (301-188) MRSA bacteremia isolates with similar genetic
background (sequence type 45 [ST45]) will help us to better
understand underlying mechanisms of persistent MRSA bacteremia.",
journal = "Genome Announc.",
volume = 2,
number = 2,
month = mar,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Velusamy2014-ja,
title = "Draft Genome Sequences of Staphylococcus aureus {AMRF1} ({ST22})
and {AMRF2} ({ST672)}, Ocular {Methicillin-Resistant} Isolates",
author = "Velusamy, Nithya and Prakash, Logambiga and Sivakumar, Neelamegam
and Antony, Aju and Prajna, Lalitha and Mohankumar, Vidyarani and
Devarajan, Bharanidharan",
abstract = "Sequence type 22 (ST22) and ST672 are the two major emerging
clones of community-acquired methicillin-resistant Staphylococcus
aureus in India. ST672 strains were found to cause severe ocular
infections. We report the draft genome sequences of two emerging
strains of methicillin-resistant S. aureus, AMRF1 (ST22) and
AMRF2 (ST672), isolated from patients with ocular infections.",
journal = "Genome Announc.",
volume = 2,
number = 2,
month = mar,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Gill2014-ui,
title = "Revised Genome Sequence of Staphylococcus aureus Bacteriophage
{K}",
author = "Gill, Jason J",
abstract = "Bacteriophage K is a member of the virulent Twort-like group of
myophages infecting Staphylococcus aureus. The revised sequence
presented here includes 12,436 bp of additional sequence not
present in the previously available phage K genome (GenBank
accession no. NC\_005880) and updated annotations, and has been
reopened at the predicted terminal repeat boundary.",
journal = "Genome Announc.",
volume = 2,
number = 1,
month = jan,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Wang2014-mb,
title = "Genome Sequence of Staphylococcus aureus Strain {LCT-SA67}, a
Space Flight Strain with Altered Carbon Source Utilization
Properties",
author = "Wang, Junfeng and Li, Yinhu and Guo, Jun and Zhang, Xuelin and
Guo, Yinghua and Chang, De and Li, Tianzhi and Xu, Guogang and
Dai, Wenkui and Liu, Changting",
abstract = "An increasing number of studies have confirmed that space flight
environments can have a significant effect on a variety of
microbial properties. To explore the effect of these environments
on Staphylococcus aureus, we present the draft genome sequence of
an S. aureus strain, named LCT-SA67, which was isolated after
space flight.",
journal = "Genome Announc.",
volume = 2,
number = 1,
month = feb,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Jia2013-jj,
title = "Complete Genome Sequence of Staphylococcus aureus Siphovirus
Phage {JS01}",
author = "Jia, Hongying and Bai, Qinqin and Yang, Yongchun and Yao, Huochun",
abstract = "Staphylococcus aureus is the most prevalent and economically
significant pathogen causing bovine mastitis. We isolated and
characterized one staphylophage from the milk of
mastitis-affected cattle and sequenced its genome. Transmission
electron microscopy (TEM) observation shows that it belongs to
the family Siphovirus. We announce here its complete genome
sequence and report major findings from the genomic analysis.",
journal = "Genome Announc.",
volume = 1,
number = 6,
month = nov,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Sabirova2014-ac,
title = "Complete Genome Sequences of Two Prolific {Biofilm-Forming}
Staphylococcus aureus Isolates Belonging to {USA300} and
{EMRSA-15} Clonal Lineages",
author = "Sabirova, J S and Xavier, B B and Hernalsteens, J-P and De Greve,
H and Ieven, M and Goossens, H and Malhotra-Kumar, S",
abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) causes serious
infections that are even more difficult to treat when associated
with a biofilm phenotype that facilitates evasion of the host
immune system and antibiotics. As a first step toward
understanding the mechanisms underlying biofilm formation, we
sequenced the genomes of two prolific biofilm-forming strains
belonging to the two most important globally disseminated clonal
lineages, USA300 and EMRSA-15.",
journal = "Genome Announc.",
volume = 2,
number = 3,
month = jun,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Murali2014-ap,
title = "Genome Sequences of Four Clinical Staphylococcus aureus Strains
with Diverse Drug Resistance Profiles Isolated from Diabetic Foot
Ulcers",
author = "Murali, Thokur Sreepathy and Paul, Bobby and Parikh, Hersh and
Singh, Rana Pratap and Kavitha, Shettigar and Bhat, Manoj K and
Satyamoorthy, Kapaettu",
abstract = "Staphylococcus aureus is a major pathogen associated with
diabetic foot ulcer infections. To gain insight into their
pathogenicity and virulence potential, we report draft genome
sequences of four strains of Staphylococcus aureus, isolated from
diabetic foot ulcers, showing profiles with various degrees of
resistance to common antibiotics.",
journal = "Genome Announc.",
volume = 2,
number = 2,
month = mar,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Kim2014-bx,
title = "Genome sequence of type strain of Staphylococcus aureus subsp.
aureus",
author = "Kim, Bong-Soo and Yi, Hana and Chun, Jongsik and Cha, Chang-Jun",
abstract = "BACKGROUND: Staphylococcus aureus is a pathogen that causes food
poisoning and community-associated infection with antibiotic
resistance. This species is an indigenous intestinal microbe
found in infants and not found in adult intestine. The relatively
small genome size and rapid evolution of antibiotic resistance
genes in the species have been drawing an increasing attention in
public health. To extend our understanding of the species and use
the genome data for comparative genomic studies, we sequenced the
type strain of S. aureus subsp. aureus DSM 20231T. RESULTS:
Seventeen contigs were generated using hybrid assembly of
sequences derived from the Roche 454 and Illumina systems. The
length of the genome sequence was 2,902,619 bases with a G + C
content of 32.8\%. Among the 2,550 annotated CDSs, 44 CDSs were
annotated to antibiotic resistance genes and 13 CDSs were related
to methicillin resistance. It is interesting to note that this
strain was first isolated in 1884 before methicillin was
generally used on patients. CONCLUSIONS: The present study
analyzed the genome sequence of S. aureus subsp. aureus type
strain as the reference sequence for comparative genomic analyses
of clinical isolates. Methicillin resistance genes found in the
genome indicate the presence of antibiotic resistance mechanism
prior to the usage of antibiotics. Further comparative genomic
studies of methicillin-resistant strains based on this reference
genome would help to understand the evolution of resistance
mechanism and dissemination of resistance genes.",
journal = "Gut Pathog.",
volume = 6,
number = 1,
pages = "6",
month = mar,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Tobes2013-xp,
title = "Noncontiguous Finished Genome Sequence of Staphylococcus aureus
{KLT6}, a Staphylococcal Enterotoxin {B-Positive} Strain Involved
in a Food Poisoning Outbreak in Switzerland",
author = "Tobes, Raquel and Manrique, Marina and Brozynska, Marta and
Stephan, Roger and Pareja, Eduardo and Johler, Sophia",
abstract = "We present the first complete genome sequence of a Staphylococcus
aureus strain assigned to clonal complex 12. The strain was
isolated in a food poisoning outbreak due to contaminated potato
salad in Switzerland in 2009, and it produces staphylococcal
enterotoxin B.",
journal = "Genome Announc.",
volume = 1,
number = 3,
month = may,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Stegger2013-hj,
title = "Genome Sequence of Staphylococcus aureus Strain {CA-347}, a
{USA600} {Methicillin-Resistant} Isolate",
author = "Stegger, Marc and Driebe, Elizabeth M and Roe, Chandler and
Lemmer, Darrin and Bowers, Jolene R and Engelthaler, David M and
Keim, Paul and Andersen, Paal S",
abstract = "The Staphylococcus aureus clonal lineage CC45 is a predominant
colonizer of healthy individuals in northern Europe and
constitutes a highly basal cluster of the S. aureus population.
Here, we report the complete genome sequence of S. aureus strain
CA-347 (NRS648), a representative of the methicillin-resistant
USA600 clone predominantly found in the United States.",
journal = "Genome Announc.",
volume = 1,
number = 4,
month = jul,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Chen2013-df,
title = "Complete genome sequence of Staphylococcus aureus Z172, a
vancomycin-intermediate and daptomycin-nonsusceptible
methicillin-resistant strain isolated in Taiwan",
author = "Chen, Feng-Jui and Lauderdale, Tsai-Ling and Wang, Lih-Shinn and
Huang, I-Wen",
abstract = "ABSTRACT We report the complete genome sequence of Z172, a
representative strain of sequence type 239-staphylococcal
cassette chromosome mec type III (ST239-SCCmec type III)
hospital-associated methicillin-resistant Staphylococcus aureus
in Taiwan. Strain Z172 ...",
journal = "Genome Announc.",
publisher = "Am Soc Microbiol",
volume = 1,
number = 6,
pages = "e01011--13",
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{McDonald2013-xz,
title = "Draft Genome Sequence of {Methicillin-Susceptible} Staphylococcus
aureus Strain {06BA18369}, a Pathogen Associated with Skin and
Soft Tissue Infections in Northern Saskatchewan, Canada",
author = "McDonald, Ryan R and Golding, George R and Irvine, James and
Graham, Morag R and Tyler, Shaun and Mulvey, Michael R and
Levett, Paul N",
abstract = "Here, we announce the draft sequence of a representative
methicillin-susceptible Staphylococcus aureus (MSSA) isolate
(06BA18369) whose strain type (spa type t311) was commonly
isolated from skin and soft tissue coinfections with
Streptococcus pyogenes. This strain sequence provides insight
into a highly successful community-associated MSSA strain type.",
journal = "Genome Announc.",
volume = 1,
number = 3,
month = jun,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Corvaglia2013-gt,
title = "{Whole-Genome} Sequences of Two Staphylococcus aureus {ST398}
Strains of Human Origin, {S94} and {S100}",
author = "Corvaglia, Anna-Rita and Fran{\c c}ois, Patrice and Bertrand,
Xavier and Quentin, Roland and Hernandez, David and van der
Mee-Marquet, Nathalie",
abstract = "Sequence type 398 (ST398) Staphylococcus aureus was originally
associated with animal infection. We announce the complete genome
sequences of two ST398 methicillin-susceptible S. aureus strains
of human origin, S94 and S100. The genome sequences assist in the
characterization of interesting ST398 features related to host
specificities.",
journal = "Genome Announc.",
volume = 1,
number = 5,
month = aug,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Fraunholz2013-le,
title = "Complete Genome Sequence of Staphylococcus aureus 6850, a Highly
Cytotoxic and Clinically Virulent {Methicillin-Sensitive} Strain
with Distant Relatedness to Prototype Strains",
author = "Fraunholz, Martin and Bernhardt, J{\"o}rg and Schuldes, J{\"o}rg
and Daniel, Rolf and Hecker, Michael and Sinha, Bhanu",
abstract = "Staphylococcus aureus is a frequent human commensal bacterium and
pathogen. Here we report the complete genome sequence of strain
6850 (spa type t185; sequence type 50 [ST50]), a highly cytotoxic
and clinically virulent methicillin-sensitive strain from a
patient with complicated S. aureus bacteremia associated with
osteomyelitis and septic arthritis.",
journal = "Genome Announc.",
volume = 1,
number = 5,
month = sep,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Harro2013-ua,
title = "Draft Genome Sequence of the {Methicillin-Resistant}
Staphylococcus aureus Isolate {MRSA-M2}",
author = "Harro, Janette M and Daugherty, Sean and Bruno, Vincent M and
Jabra-Rizk, Mary Ann and Rasko, David A and Shirtliff, Mark E",
abstract = "We report the draft genome sequence of a methicillin-resistant
strain of Staphylococcus aureus, designated MRSA-M2. This
clinical isolate was obtained from an osteomyelitis patient
undergoing treatment at the University of Texas Medical Branch
(Galveston, TX). This strain is an ST30, spa type T019, agr III
strain and has been utilized as a model S. aureus strain in a
number of proteomic, transcriptomic, and animal model studies.",
journal = "Genome Announc.",
volume = 1,
number = 1,
month = jan,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Hernandez2014-ul,
title = "De novo finished 2.8 Mbp Staphylococcus aureus genome assembly
from 100 bp short and long range paired-end reads",
author = "Hernandez, David and Tewhey, Ryan and Veyrieras, Jean-Baptiste
and Farinelli, Laurent and {\O}ster{\aa}s, Magne and Fran{\c
c}ois, Patrice and Schrenzel, Jacques",
abstract = "MOTIVATION: Paired-end sequencing allows circumventing the
shortness of the reads produced by second generation sequencers
and is essential for de novo assembly of genomes. However,
obtaining a finished genome from short reads is still an open
challenge. We present an algorithm that exploits the pairing
information issued from inserts of potentially any length. The
method determines paths through an overlaps graph by using a
constrained search tree. We also present a method that
automatically determines suited overlaps cutoffs according to the
contextual coverage, reducing thus the need for manual
parameterization. Finally, we introduce an interactive mode that
allows querying an assembly at targeted regions. RESULTS: We
assess our methods by assembling two Staphylococcus aureus
strains that were sequenced on the Illumina platform. Using 100
bp paired-end reads and minimal manual curation, we produce a
finished genome sequence for the previously undescribed isolate
SGH-10-168. AVAILABILITY AND IMPLEMENTATION: The presented
algorithms are implemented in the standalone Edena software,
freely available under the General Public License (GPLv3) at
www.genomic.ch/edena.php.",
journal = "Bioinformatics",
volume = 30,
number = 1,
pages = "40--49",
month = jan,
year = 2014,
keywords = "Staphylococcus;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Golubchik2013-cy,
title = "Within-host evolution of Staphylococcus aureus during
asymptomatic carriage",
author = "Golubchik, Tanya and Batty, Elizabeth M and Miller, Ruth R and
Farr, Helen and Young, Bernadette C and Larner-Svensson, Hanna
and Fung, Rowena and Godwin, Heather and Knox, Kyle and
Votintseva, Antonina and Everitt, Richard G and Street, Teresa
and Cule, Madeleine and Ip, Camilla L C and Didelot, Xavier and
Peto, Timothy E A and Harding, Rosalind M and Wilson, Daniel J
and Crook, Derrick W and Bowden, Rory",
abstract = "BACKGROUND: Staphylococcus aureus is a major cause of healthcare
associated mortality, but like many important bacterial
pathogens, it is a common constituent of the normal human body
flora. Around a third of healthy adults are carriers. Recent
evidence suggests that evolution of S. aureus during nasal
carriage may be associated with progression to invasive disease.
However, a more detailed understanding of within-host evolution
under natural conditions is required to appreciate the
evolutionary and mechanistic reasons why commensal bacteria such
as S. aureus cause disease. Therefore we examined in detail the
evolutionary dynamics of normal, asymptomatic carriage.
Sequencing a total of 131 genomes across 13 singly colonized
hosts using the Illumina platform, we investigated diversity,
selection, population dynamics and transmission during the
short-term evolution of S. aureus. PRINCIPAL FINDINGS: We
characterized the processes by which the raw material for
evolution is generated: micro-mutation (point mutation and small
insertions/deletions), macro-mutation (large
insertions/deletions) and the loss or acquisition of mobile
elements (plasmids and bacteriophages). Through an analysis of
synonymous, non-synonymous and intergenic mutations we
discovered a fitness landscape dominated by purifying selection,
with rare examples of adaptive change in genes encoding
surface-anchored proteins and an enterotoxin. We found evidence
for dramatic, hundred-fold fluctuations in the size of the
within-host population over time, which we related to the cycle
of colonization and clearance. Using a newly-developed
population genetics approach to detect recent transmission among
hosts, we revealed evidence for recent transmission between some
of our subjects, including a husband and wife both carrying
populations of methicillin-resistant S. aureus (MRSA).
SIGNIFICANCE: This investigation begins to paint a picture of
the within-host evolution of an important bacterial pathogen
during its prevailing natural state, asymptomatic carriage.
These results also have wider significance as a benchmark for
future systematic studies of evolution during invasive S. aureus
disease.",
journal = "PLoS One",
publisher = "Public Library of Science",
volume = 8,
number = 5,
pages = "e61319",
month = may,
year = 2013,
keywords = "evolution;colonization;Staphylococcus;within-host-evolution;Staph\_evolutionary\_history/USA300\_evolution;Staph\_evolutionary\_history;imported\_from\_papers\_14Nov2013;Staph\_evolutionary\_history/Staph\_population\_dynamics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Suzuki2012-cj,
title = "Comparative genomic analysis of the genus Staphylococcus
including Staphylococcus aureus and its newly described sister
species Staphylococcus simiae",
author = "Suzuki, Haruo and Lef{\'e}bure, Tristan and Bitar, Paulina
Pavinski and Stanhope, Michael J",
abstract = "BACKGROUND:Staphylococcus belongs to the Gram-positive low G + C
content group of the Firmicutes division of bacteria.
Staphylococcus aureus is an important human and veterinary
pathogen that causes a broad spectrum of diseases, and has
developed important multidrug resistant forms such as
methicillin-resistant S. aureus (MRSA). Staphylococcus simiae
was isolated from South American squirrel monkeys in 2000, and
is a coagulase-negative bacterium, closely related, and possibly
the sister group, to S. aureus. Comparative genomic analyses of
closely related bacteria with different phenotypes can provide
information relevant to understanding adaptation to host
environment and mechanisms of pathogenicity.RESULTS:We
determined a Roche/454 draft genome sequence for S. simiae and
included it in comparative genomic analyses with 11 other
Staphylococcus species including S. aureus. A genome based
phylogeny of the genus confirms that S. simiae is the sister
group to S. aureus and indicates that the most basal
Staphylococcus lineage is Staphylococcus pseudintermedius,
followed by Staphylococcus carnosus. Given the primary niche of
these two latter taxa, compared to the other species in the
genus, this phylogeny suggests that human adaptation evolved
after the split of S. carnosus. The two coagulase-positive
species (S. aureus and S. pseudintermedius) are not
phylogenetically closest but share many virulence factors
exclusively, suggesting that these genes were acquired by
horizontal transfer. Enrichment in genes related to mobile
elements such as prophage in S. aureus relative to S. simiae
suggests that pathogenesis in the S. aureus group has developed
by gene gain through horizontal transfer, after the split of S.
aureus and S. simiae from their common
ancestor.CONCLUSIONS:Comparative genomic analyses across 12
Staphylococcus species provide hypotheses about lineages in
which human adaptation has taken place and contributions of
horizontal transfer in pathogenesis.",
journal = "BMC Genomics",
publisher = "BioMed Central Ltd",
volume = 13,
pages = "38",
year = 2012,
keywords = "Staphylococcus;imported\_from\_papers\_14Nov2013;bacterial
comparative genomics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Everitt2014-tp,
title = "Mobile elements drive recombination hotspots in the core genome
of Staphylococcus aureus",
author = "Everitt, Richard G and Didelot, Xavier and Batty, Elizabeth M and
Miller, Ruth R and Knox, Kyle and Young, Bernadette C and Bowden,
Rory and Auton, Adam and Votintseva, Antonina and
Larner-Svensson, Hanna and Charlesworth, Jane and Golubchik,
Tanya and Ip, Camilla L C and Godwin, Heather and Fung, Rowena
and Peto, Tim E A and Walker, A Sarah and Crook, Derrick W and
Wilson, Daniel J",
abstract = "Horizontal gene transfer is an important driver of bacterial
evolution, but genetic exchange in the core genome of clonal
species, including the major pathogen Staphylococcus aureus, is
incompletely understood. Here we reveal widespread homologous
recombination in S. aureus at the species level, in contrast to
its near-complete absence between closely related strains. We
discover a patchwork of hotspots and coldspots at fine scales
falling against a backdrop of broad-scale trends in rate
variation. Over megabases, homoplasy rates fluctuate 1.9-fold,
peaking towards the origin-of-replication. Over kilobases, we
find core recombination hotspots of up to 2.5-fold enrichment
situated near fault lines in the genome associated with mobile
elements. The strongest hotspots include regions flanking
conjugative transposon ICE6013, the staphylococcal cassette
chromosome (SCC) and genomic island $\nu$Sa$\alpha$. Mobile
element-driven core genome transfer represents an opportunity for
adaptation and challenges our understanding of the recombination
landscape in predominantly clonal pathogens, with important
implications for genotype-phenotype mapping.",
journal = "Nat. Commun.",
volume = 5,
pages = "3956",
month = may,
year = 2014,
keywords = "
Staphylococcus;evolution;teaching-tutorial;recombination;bacterial
comparative
genomics;Staph\_evolutionary\_history;Staph\_evolutionary\_history/Teaching\_Prokaryotic\_evolution;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Holt2011-bo,
title = "A Very {Early-Branching} Staphylococcus aureus Lineage Lacking
the Carotenoid Pigment Staphyloxanthin",
author = "Holt, D C and Holden, M T G and Tong, S Y C and Castillo-Ramirez,
S and Clarke, L and Quail, M A and Currie, B J and Parkhill, J
and Bentley, S D and Feil, E J and Giffard, P M",
journal = "Genome Biol. Evol.",
volume = 3,
number = 0,
pages = "881--895",
year = 2011,
keywords = "Staphylococcus;imported\_from\_papers\_14Nov2013;Staph\_evolutionary\_history;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Koch2014-bi,
title = "Evolution of Resistance to a {Last-Resort} Antibiotic in
Staphylococcus aureus via Bacterial Competition",
author = "Koch, Gudrun and Yepes, Ana and F{\"o}rstner, Konrad U and
Wermser, Charlotte and Stengel, Stephanie T and Modamio, Jennifer
and Ohlsen, Knut and Foster, Kevin R and Lopez, Daniel",
abstract = "Antibiotic resistance is a key medical concern, with antibiotic
use likely being an important cause. However, here we describe an
alternative route to clinically relevant antibiotic resistance
that occurs solely due to competitive interactions among
bacterial cells. We consistently observe that isolates of
Methicillin-resistant Staphylococcus aureus diversify
spontaneously into two distinct, sequentially arising strains.
The first evolved strain outgrows the parent strain via secretion
of surfactants and a toxic bacteriocin. The second is resistant
to the bacteriocin. Importantly, this second strain is also
resistant to intermediate levels of vancomycin. This so-called
VISA (vancomycin-intermediate S. aureus) phenotype is seen in
many hard-to-treat clinical isolates. This strain diversification
also occurs during in vivo infection in a mouse model, which is
consistent with the fact that both coevolved phenotypes resemble
strains commonly found in clinic. Our study shows how competition
between coevolving bacterial strains can generate antibiotic
resistance and recapitulate key clinical phenotypes.",
journal = "Cell",
volume = 158,
number = 5,
pages = "1060--1071",
month = aug,
year = 2014,
keywords = "
antibiotics;Staphylococcus;Staph\_evolutionary\_history;bacterial
comparative
genomics;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Benson2014-jp,
title = "Evolution of hypervirulence by a {MRSA} clone through acquisition
of a transposable element",
author = "Benson, Meredith A and Ohneck, Elizabeth A and Ryan, Chanelle and
Alonzo, 3rd, Francis and Smith, Hannah and Narechania, Apurva and
Kolokotronis, Sergios-Orestis and Satola, Sarah W and Uhlemann,
Anne-Catrin and Sebra, Robert and Deikus, Gintaras and Shopsin,
Bo and Planet, Paul J and Torres, Victor J",
abstract = "Staphylococcus aureus has evolved as a pathogen that causes a
range of diseases in humans. There are two dominant modes of
evolution thought to explain most of the virulence differences
between strains. First, virulence genes may be acquired from
other organisms. Second, mutations may cause changes in the
regulation and expression of genes. Here we describe an
evolutionary event in which transposition of an IS element has a
direct impact on virulence gene regulation resulting in
hypervirulence. Whole-genome analysis of a methicillin-resistant
S. aureus (MRSA) strain USA500 revealed acquisition of a
transposable element (IS256) that is absent from close relatives
of this strain. Of the multiple copies of IS256 found in the
USA500 genome, one was inserted in the promoter sequence of
repressor of toxins (Rot), a master transcriptional regulator
responsible for the expression of virulence factors in S. aureus.
We show that insertion into the rot promoter by IS256 results in
the derepression of cytotoxin expression and increased virulence.
Taken together, this work provides new insight into evolutionary
strategies by which S. aureus is able to modify its virulence
properties and demonstrates a novel mechanism by which horizontal
gene transfer directly impacts virulence through altering toxin
regulation.",
journal = "Mol. Microbiol.",
volume = 93,
number = 4,
pages = "664--681",
month = aug,
year = 2014,
keywords = "Staphylococcus;toxicity;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers"
}
@ARTICLE{Chua2014-sh,
title = "Hyperexpression of alpha-hemolysin explains enhanced virulence of
sequence type 93 community-associated methicillin-resistant
Staphylococcus aureus",
author = "Chua, Kyra and Monk, Ian and Lin, Ya-Hsun and Seemann, Torsten
and Tuck, Kellie and Porter, Jessica and Stepnell, Justin and
Coombs, Geoffrey and Davies, John and Stinear, Timothy and
Howden, Benjamin",
abstract = "BACKGROUND:The community-associated methicillin-resistant S.
aureus (CA-MRSA) ST93 clone is becoming dominant in Australia and
is clinically highly virulent. In addition, sepsis and skin
infection models demonstrate that ST93 CA-MRSA is the most
virulent global clone of S. aureus tested to date. While the
determinants of virulence have been studied in other clones of
CA-MRSA, the basis for hypervirulence in ST93 CA-MRSA has not
been defined.RESULTS:Here, using a geographically and temporally
dispersed collection of ST93 isolates we demonstrate that the
ST93 population hyperexpresses key CA-MRSA exotoxins, in
particular alpha-hemolysin, in comparison to other global clones.
Gene deletion and complementation studies, and virulence
comparisons in a murine skin infection model, showed
unequivocally that increased expression of alpha-hemolysin is the
key staphylococcal virulence determinant for this clone. Genome
sequencing and comparative genomics of strains with divergent
exotoxin profiles demonstrated that, like other S. aureus clones,
the quorum sensing agr system is the master regulator of toxin
expression and virulence in ST93 CA-MRSA. However, we also
identified a previously uncharacterized AraC/XylS family
regulator (AryK) that potentiates toxin expression and virulence
in S. aureus.CONCLUSIONS:These data demonstrate that
hyperexpression of alpha-hemolysin mediates enhanced virulence in
ST93 CA-MRSA, and additional control of exotoxin production, in
particular alpha-hemolysin, mediated by regulatory systems other
than agr have the potential to fine-tune virulence in CA-MRSA.",
journal = "BMC Microbiol.",
volume = 14,
number = 1,
pages = "31",
year = 2014,
keywords = "Staphylococcus;toxicity;antibiotics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Long2014-hn,
title = "Absence of {Patient-to-Patient} Intrahospital Transmission of
Staphylococcus aureus as Determined by {Whole-Genome} Sequencing",
author = "Long, S Wesley and Beres, Stephen B and Olsen, Randall J and
Musser, James M",
abstract = "Nosocomial transmission of pathogens is a major health care
challenge. The increasing spread of antibiotic-resistant strains
represents an ongoing threat to public health. Previous
Staphylococcus aureus transmission studies have focused on
transmission of S. aureus between asymptomatic carriers or used
low-resolution typing methods such as multilocus sequence typing
(MLST) or spa typing. To identify patient-to-patient
intrahospital transmission using high-resolution genetic
analysis, we sequenced the genomes of a consecutive set of 398 S.
aureus isolates from sterile-site infections. The S. aureus
strains were collected from four hospitals in the Houston
Methodist Hospital System over a 6-month period. Importantly, we
discovered no evidence of transmission of S. aureus between
patients with sterile-site infections. The lack of intrahospital
transmission may reflect a fundamental difference between
day-to-day transmission events in the hospital setting and the
more frequently studied outbreak scenarios.IMPORTANCE Previous
studies have suggested that nosocomial transmission of S. aureus
is common. Our data revealed an unexpected lack of evidence for
intrahospital transmission of S. aureus between patients with
invasive infections. This finding has important implications for
hospital infection control and public health efforts. In
addition, our data demonstrate that highly related pools of S.
aureus strains exist in the community which may complicate
outbreak investigations.",
journal = "MBio",
volume = 5,
number = 5,
month = oct,
year = 2014,
keywords = "Staphylococcus;bacterial comparative
genomics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Parker2014-bc,
title = "Genome Sequence of Bacterial Interference Strain Staphylococcus
aureus {502A}",
author = "Parker, Dane and Narechania, Apurva and Sebra, Robert and Deikus,
Gintaras and Larussa, Samuel and Ryan, Chanelle and Smith, Hannah
and Prince, Alice and Mathema, Barun and Ratner, Adam J and
Kreiswirth, Barry and Planet, Paul J",
abstract = "Staphylococcus aureus 502A was a strain used in bacterial
interference programs during the 1960s and early 1970s. Infants
were deliberately colonized with 502A with the goal of preventing
colonization with more invasive strains. We present the completed
genome sequence of this organism.",
journal = "Genome Announc.",
volume = 2,
number = 2,
month = apr,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Gordon2014-jf,
title = "Prediction of Staphylococcus aureus antimicrobial resistance by
whole-genome sequencing",
author = "Gordon, N C and Price, J R and Cole, K and Everitt, R and Morgan,
M and Finney, J and Kearns, A M and Pichon, B and Young, B and
Wilson, D J and Llewelyn, M J and Paul, J and Peto, T E A and
Crook, D W and Walker, A S and Golubchik, T",
abstract = "Whole-genome sequencing (WGS) could potentially provide a single
platform for extracting all the information required to predict
an organism's phenotype. However, its ability to provide accurate
predictions has not yet been demonstrated in large independent
studies of specific organisms. In this study, we aimed to develop
a genotypic prediction method for antimicrobial susceptibilities.
The whole genomes of 501 unrelated Staphylococcus aureus isolates
were sequenced, and the assembled genomes were interrogated using
BLASTn for a panel of known resistance determinants (chromosomal
mutations and genes carried on plasmids). Results were compared
with phenotypic susceptibility testing for 12 commonly used
antimicrobial agents (penicillin, methicillin, erythromycin,
clindamycin, tetracycline, ciprofloxacin, vancomycin,
trimethoprim, gentamicin, fusidic acid, rifampin, and mupirocin)
performed by the routine clinical laboratory. We investigated
discrepancies by repeat susceptibility testing and manual
inspection of the sequences and used this information to optimize
the resistance determinant panel and BLASTn algorithm. We then
tested performance of the optimized tool in an independent
validation set of 491 unrelated isolates, with phenotypic results
obtained in duplicate by automated broth dilution (BD Phoenix)
and disc diffusion. In the validation set, the overall
sensitivity and specificity of the genomic prediction method were
0.97 (95\% confidence interval [95\% CI], 0.95 to 0.98) and 0.99
(95\% CI, 0.99 to 1), respectively, compared to standard
susceptibility testing methods. The very major error rate was
0.5\%, and the major error rate was 0.7\%. WGS was as sensitive
and specific as routine antimicrobial susceptibility testing
methods. WGS is a promising alternative to culture methods for
resistance prediction in S. aureus and ultimately other major
bacterial pathogens.",
journal = "J. Clin. Microbiol.",
volume = 52,
number = 4,
pages = "1182--1191",
month = apr,
year = 2014,
keywords = "antibiotics;Staphylococcus;Teaching antibiotic resistance
genomics;Read-lab-shared;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers;GWAS-bacteria"
}
@ARTICLE{Dean2014-fn,
title = "Identification of point mutations in clinical Staphylococcus
aureus strains that produce small-colony variants auxotrophic for
menadione",
author = "Dean, Melissa A and Olsen, Randall J and Long, S Wesley and
Rosato, Adriana E and Musser, James M",
abstract = "Staphylococcus aureus small-colony variants (SCVs) are implicated
in chronic and relapsing infections that are difficult to
diagnose and treat. Despite many years of study, the underlying
molecular mechanisms and virulence effect of the small-colony
phenotype remain incompletely understood. We sequenced the
genomes of five S. aureus SCV strains recovered from human
patients and discovered previously unidentified nonsynonymous
point mutations in three genes encoding proteins in the menadione
biosynthesis pathway. Analysis of genetic revertants and
complementation with wild-type alleles confirmed that these
mutations caused the SCV phenotype and decreased virulence for
mice.",
journal = "Infect. Immun.",
volume = 82,
number = 4,
pages = "1600--1605",
month = apr,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{McCarthy2014-np,
title = "Extensive horizontal gene transfer during Staphylococcus aureus
co-colonization in vivo",
author = "McCarthy, Alex J and Loeffler, Anette and Witney, Adam A and
Gould, Katherine A and Lloyd, David H and Lindsay, Jodi A",
abstract = "Staphylococcus aureus is a commensal and major pathogen of humans
and animals. Comparative genomics of S. aureus populations
suggests that colonization of different host species is
associated with carriage of mobile genetic elements (MGE),
particularly bacteriophages and plasmids capable of encoding
virulence, resistance, and immune evasion pathways.
Antimicrobial-resistant S. aureus of livestock are a potential
zoonotic threat to human health if they adapt to colonize humans
efficiently. We utilized the technique of experimental evolution
and co-colonized gnotobiotic piglets with both human- and
pig-associated variants of the lineage clonal complex 398, and
investigated growth and genetic changes over 16 days using whole
genome sequencing. The human isolate survived co-colonization on
piglets more efficiently than in vitro. During co-colonization,
transfer of MGE from the pig to the human isolate was detected
within 4 h. Extensive and repeated transfer of two bacteriophages
and three plasmids resulted in colonization with isolates
carrying a wide variety of mobilomes. Whole genome sequencing of
progeny bacteria revealed no acquisition of core genome
polymorphisms, highlighting the importance of MGE. Staphylococcus
aureus bacteriophage recombination and integration into novel
sites was detected experimentally for the first time. During
colonization, clones coexisted and diversified rather than a
single variant dominating. Unexpectedly, each piglet carried
unique populations of bacterial variants, suggesting limited
transmission of bacteria between piglets once colonized. Our data
show that horizontal gene transfer occurs at very high frequency
in vivo and significantly higher than that detectable in vitro.",
journal = "Genome Biol. Evol.",
volume = 6,
number = 10,
pages = "2697--2708",
month = oct,
year = 2014,
keywords = "bacteriophage; experimental evolution; host adaptation; plasmid;
population
dynamics;Staphylococcus;colonization;recombination;Staph\_evolutionary\_history/Staph\_population\_dynamics;Staph\_evolutionary\_history/staph
microbial interactions;bacterial comparative
genomics;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
}
@ARTICLE{Kobayashi2012-he,
title = "Genomic analysis of the emergence of vancomycin-resistant
Staphylococcus aureus",
author = "Kobayashi, Scott D and Musser, James M and DeLeo, Frank R",
abstract = "Staphylococcus aureus is a human commensal bacterium and a
prominent cause of infections globally. The high incidence of S.
aureus infections is compounded by the ability of the microbe to
readily acquire resistance to antibiotics. In the United States,
methicillin-resistant S. aureus (MRSA) is a leading cause of
morbidity and mortality by a single infectious agent. Therapeutic
options for severe MRSA infections are limited to a few
antibiotics to which the organism is typically susceptible,
including vancomycin. Acquisition of high-level vancomycin
resistance by MRSA is a major concern, but to date, there have
been only 12 vancomycin-resistant S. aureus (VRSA) isolates
reported in the United States and all belong to a phylogenetic
lineage known as clonal complex 5. To gain enhanced understanding
of the genetic characteristics conducive to the acquisition of
vancomycin resistance by S. aureus, V. N. Kos et al. performed
whole-genome sequencing of all 12 VRSA isolates and compared the
DNA sequences to the genomes of other S. aureus strains. The
findings provide new information about the evolutionary history
of VRSA and identify genetic features that may bear on the
relationship between S. aureus clonal complex 5 strains and the
acquisition of vancomycin resistance genes from enterococci.",
journal = "MBio",
volume = 3,
number = 4,
month = jun,
year = 2012,
keywords = "Staphylococcus;antibiotcs-evolution-fitness;MRSA-VRSA-gene\_transfer;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Holden2013-bu,
title = "A genomic portrait of the emergence, evolution, and global spread
of a methicillin-resistant Staphylococcus aureus pandemic",
author = "Holden, Matthew T G and Hsu, Li Yang and Kurt, Kevin and Weinert,
Lucy A and Mather, Alison E and Harris, Simon R and Strommenger,
Birgit and Layer, Franziska and Witte, Wolfgang and de Lencastre,
Herminia and Skov, Robert and Westh, Henrik and Zemlickov{\'a},
Helena and Coombs, Geoffrey and Kearns, Angela M and Hill, Robert
L R and Edgeworth, Jonathan and Gould, Ian and Gant, Vanya and
Cooke, Jonathan and Edwards, Giles F and McAdam, Paul R and
Templeton, Kate E and McCann, Angela and Zhou, Zhemin and
Castillo-Ram{\'\i}rez, Santiago and Feil, Edward J and Hudson,
Lyndsey O and Enright, Mark C and Balloux, Francois and Aanensen,
David M and Spratt, Brian G and Fitzgerald, J Ross and Parkhill,
Julian and Achtman, Mark and Bentley, Stephen D and N{\"u}bel,
Ulrich",
abstract = "The widespread use of antibiotics in association with
high-density clinical care has driven the emergence of
drug-resistant bacteria that are adapted to thrive in
hospitalized patients. Of particular concern are globally
disseminated methicillin-resistant Staphylococcus aureus (MRSA)
clones that cause outbreaks and epidemics associated with health
care. The most rapidly spreading and tenacious
health-care-associated clone in Europe currently is EMRSA-15,
which was first detected in the UK in the early 1990s and
subsequently spread throughout Europe and beyond. Using
phylogenomic methods to analyze the genome sequences for 193 S.
aureus isolates, we were able to show that the current pandemic
population of EMRSA-15 descends from a health-care-associated
MRSA epidemic that spread throughout England in the 1980s, which
had itself previously emerged from a primarily
community-associated methicillin-sensitive population. The
emergence of fluoroquinolone resistance in this EMRSA-15 subclone
in the English Midlands during the mid-1980s appears to have
played a key role in triggering pandemic spread, and occurred
shortly after the first clinical trials of this drug.
Genome-based coalescence analysis estimated that the population
of this subclone over the last 20 yr has grown four times faster
than its progenitor. Using comparative genomic analysis we
identified the molecular genetic basis of 99.8\% of the
antimicrobial resistance phenotypes of the isolates, highlighting
the potential of pathogen genome sequencing as a diagnostic tool.
We document the genetic changes associated with adaptation to the
hospital environment and with increasing drug resistance over
time, and how MRSA evolution likely has been influenced by
country-specific drug use regimens.",
journal = "Genome Res.",
volume = 23,
number = 4,
pages = "653--664",
year = 2013,
keywords = "
Staphylococcus;antibiotics;imported\_from\_papers\_14Nov2013;Staph\_evolutionary\_history;bacterial
comparative
genomics;antibiotcs-evolution-fitness;MRSA-VRSA-gene\_transfer;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Baba2002-mu,
title = "Genome and virulence determinants of high virulence
community-acquired {MRSA}",
author = "Baba, Tadashi and Takeuchi, Fumihiko and Kuroda, Makoto and
Yuzawa, Harumi and Aoki, Ken-Ichi and Oguchi, Akio and Nagai,
Yoshimi and Iwama, Natsuko and Asano, Kazuyuki and Naimi, Timothy
and Kuroda, Hiroko and Cui, Longzhu and Yamamoto, Kenji and
Hiramatsu, Keiichi",
abstract = "BACKGROUND: A new type of meticillin-resistant Staphylococcus
aureus (MRSA), designated community-acquired MRSA, is becoming
increasingly noticeable in the community, some strains of which
cause fatal infections in otherwise healthy individuals. By
contrast with hospital-acquired MRSA, community-acquired MRSA is
more susceptible to non b-lactam antibiotics. We investigated the
high virulence potential of certain strains of this bacterium.
METHODS: We ascertained the whole genome sequence of MW2, a
strain of community-acquired MRSA, by shotgun cloning and
sequencing. MW2 caused fatal septicaemia and septic arthritis in
a 16-month-old girl in North Dakota, USA, in 1998. The genome of
this strain was compared with those of hospital-acquired MRSA
strains, including N315 and Mu50. FINDINGS: Meticillin resistance
gene (mecA) in MW2 was carried by a novel allelic form (type IVa)
of staphylococcal cassette chromosome mec (SCCmec), by contrast
with type II in N315 and Mu50. Type IVa SCCmec did not carry any
of the multiple antibiotic resistance genes reported in type II
SCCmec. By contrast, 19 additional virulence genes were recorded
in the MW2 genome. All but two of these virulence genes were
noted in four of the seven genomic islands of MW2.
INTERPRETATION: MW2 carried a range of virulence and resistance
genes that was distinct from those displayed on the chromosomes
of extant S aureus strains. Most genes were carried by specific
allelic forms of genomic islands in the MW2 chromosome. The
combination of allelic forms of genomic islands is the genetic
basis that determines the pathogenicity of medically important
phenotypes of S aureus, including those of community-acquired
MRSA strains.",
journal = "Lancet",
volume = 359,
number = 9320,
pages = "1819--1827",
month = may,
year = 2002,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Rossi2014-hc,
title = "Transferable vancomycin resistance in a community-associated
{MRSA} lineage",
author = "Rossi, Fl{\'a}via and Diaz, Lorena and Wollam, Aye and Panesso,
Diana and Zhou, Yanjiao and Rincon, Sandra and Narechania, Apurva
and Xing, Galen and Di Gioia, Thais S R and Doi, Andr{\'e} and
Tran, Truc T and Reyes, Jinnethe and Munita, Jose M and Carvajal,
Lina P and Hernandez-Roldan, Alejandra and Brand{\~a}o, Denise
and van der Heijden, Inneke Marie and Murray, Barbara E and
Planet, Paul J and Weinstock, George M and Arias, Cesar A",
abstract = "We report the case of a patient from Brazil with a bloodstream
infection caused by a strain of methicillin-resistant
Staphylococcus aureus (MRSA) that was susceptible to vancomycin
(designated BR-VSSA) but that acquired the vanA gene cluster
during antibiotic therapy and became resistant to vancomycin
(designated BR-VRSA). Both strains belong to the sequence type
(ST) 8 community-associated genetic lineage that carries the
staphylococcal chromosomal cassette mec (SCCmec) type IVa and the
S. aureus protein A gene (spa) type t292 and are phylogenetically
related to MRSA lineage USA300. A conjugative plasmid of 55,706
bp (pBRZ01) carrying the vanA cluster was identified and readily
transferred to other staphylococci. The pBRZ01 plasmid harbors
DNA sequences that are typical of the plasmid-associated
replication genes rep24 or rep21 described in
community-associated MRSA strains from Australia (pWBG745). The
presence and dissemination of community-associated MRSA
containing vanA could become a serious public health concern.",
journal = "N. Engl. J. Med.",
volume = 370,
number = 16,
pages = "1524--1531",
month = apr,
year = 2014,
keywords = "Staphylococcus;antibiotics;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Gill2005-zg,
title = "Insights on evolution of virulence and resistance from the
complete genome analysis of an early methicillin-resistant
Staphylococcus aureus strain and a biofilm-producing
methicillin-resistant Staphylococcus epidermidis strain",
author = "Gill, Steven R and Fouts, Derrick E and Archer, Gordon L and
Mongodin, Emmanuel F and Deboy, Robert T and Ravel, Jacques and
Paulsen, Ian T and Kolonay, James F and Brinkac, Lauren and
Beanan, Mauren and Dodson, Robert J and Daugherty, Sean C and
Madupu, Ramana and Angiuoli, Samuel V and Durkin, A Scott and
Haft, Daniel H and Vamathevan, Jessica and Khouri, Hoda and
Utterback, Terry and Lee, Chris and Dimitrov, George and Jiang,
Lingxia and Qin, Haiying and Weidman, Jan and Tran, Kevin and
Kang, Kathy and Hance, Ioana R and Nelson, Karen E and Fraser,
Claire M",
abstract = "Staphylococcus aureus is an opportunistic pathogen and the major
causative agent of numerous hospital- and community-acquired
infections. Staphylococcus epidermidis has emerged as a causative
agent of infections often associated with implanted medical
devices. We have sequenced the approximately 2.8-Mb genome of S.
aureus COL, an early methicillin-resistant isolate, and the
approximately 2.6-Mb genome of S. epidermidis RP62a, a
methicillin-resistant biofilm isolate. Comparative analysis of
these and other staphylococcal genomes was used to explore the
evolution of virulence and resistance between these two species.
The S. aureus and S. epidermidis genomes are syntenic throughout
their lengths and share a core set of 1,681 open reading frames.
Genome islands in nonsyntenic regions are the primary source of
variations in pathogenicity and resistance. Gene transfer between
staphylococci and low-GC-content gram-positive bacteria appears
to have shaped their virulence and resistance profiles.
Integrated plasmids in S. epidermidis carry genes encoding
resistance to cadmium and species-specific LPXTG surface
proteins. A novel genome island encodes multiple phenol-soluble
modulins, a potential S. epidermidis virulence factor. S.
epidermidis contains the cap operon, encoding the polyglutamate
capsule, a major virulence factor in Bacillus anthracis.
Additional phenotypic differences are likely the result of single
nucleotide polymorphisms, which are most numerous in cell
envelope proteins. Overall differences in pathogenicity can be
attributed to genome islands in S. aureus which encode
enterotoxins, exotoxins, leukocidins, and leukotoxins not found
in S. epidermidis.",
journal = "J. Bacteriol.",
volume = 187,
number = 7,
pages = "2426--2438",
month = apr,
year = 2005,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Diep2006-mj,
title = "Complete genome sequence of {USA300}, an epidemic clone of
community-acquired meticillin-resistant Staphylococcus aureus",
author = "Diep, Binh An and Gill, Steven R and Chang, Richard F and Phan,
Tiffany Haivan and Chen, Jason H and Davidson, Matthew G and Lin,
Felice and Lin, Jessica and Carleton, Heather A and Mongodin,
Emmanuel F and Sensabaugh, George F and Perdreau-Remington,
Fran{\c c}oise",
abstract = "BACKGROUND: USA300, a clone of meticillin-resistant
Staphylococcus aureus, is a major source of community-acquired
infections in the USA, Canada, and Europe. Our aim was to
sequence its genome and compare it with those of other strains of
S aureus to try to identify genes responsible for its distinctive
epidemiological and virulence properties. METHODS: We ascertained
the genome sequence of FPR3757, a multidrug resistant USA300
strain, by random shotgun sequencing, then compared it with the
sequences of ten other staphylococcal strains. FINDINGS: Compared
with closely related S aureus, we noted that almost all of the
unique genes in USA300 clustered in novel allotypes of mobile
genetic elements. Some of the unique genes are involved in
pathogenesis, including Panton-Valentine leucocidin and molecular
variants of enterotoxin Q and K. The most striking feature of the
USA300 genome is the horizontal acquisition of a novel mobile
genetic element that encodes an arginine deiminase pathway and an
oligopeptide permease system that could contribute to growth and
survival of USA300. We did not detect this element, termed
arginine catabolic mobile element (ACME), in other S aureus
strains. We noted a high prevalence of ACME in S epidermidis,
suggesting not only that ACME transfers into USA300 from S
epidermidis, but also that this element confers a selective
advantage to this ubiquitous commensal of the human skin.
INTERPRETATION: USA300 has acquired mobile genetic elements that
encode resistance and virulence determinants that could enhance
fitness and pathogenicity.",
journal = "Lancet",
volume = 367,
number = 9512,
pages = "731--739",
month = mar,
year = 2006,
keywords = "Staphylococcus;bacterial comparative
genomics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Viana2015-wo,
title = "A single natural nucleotide mutation alters bacterial pathogen
host tropism",
author = "Viana, David and Comos, Mar{\'\i}a and McAdam, Paul R and Ward,
Melissa J and Selva, Laura and Guinane, Caitriona M and
Gonz{\'a}lez-Mu{\~n}oz, Beatriz M and Tristan, Anne and Foster,
Simon J and Ross Fitzgerald, J and Penad{\'e}s, Jos{\'e} R",
abstract = "Jose Penades and colleagues examine host adaptation and
specificity for Staphylococcus aureus with analysis of the
whole-genome sequences of strains isolated from humans or
rabbits. They find that a rabbit-specific clone evolved through
a human-to-rabbit host jump, enabled by a single mutation in
dltB.",
journal = "Nat. Genet.",
publisher = "Nature Publishing Group",
month = feb,
year = 2015,
keywords = "Staphylococcus;colonization;bacerial\_genetics;bacterial
comparative
genomics;Staph\_evolutionary\_history;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;GWAS-bacteria;Staph\_evolution\_toxins;Staph-animal-human"
}
@ARTICLE{Ward2014-bz,
title = "{Time-Scaled} Evolutionary Analysis of the Transmission and
Antibiotic Resistance Dynamics of Staphylococcus aureus Clonal
Complex 398",
author = "Ward, M J and Gibbons, C L and McAdam, P R and van Bunnik, B A D
and Girvan, E K and Edwards, G F and Fitzgerald, J R and
Woolhouse, M E J",
abstract = "Staphylococcus aureus clonal complex 398 (CC398) is associated
with disease in humans and livestock, and its origins and
transmission have generated considerable interest. We performed a
time-scaled phylogenetic analysis of CC398, including sequenced
isolates from the United Kingdom (Scotland), along with publicly
available genomes. Using state-of-the-art methods for mapping
traits onto phylogenies, we quantified transitions between host
species to identify sink and source populations for CC398 and
employed a novel approach to investigate the gain and loss of
antibiotic resistance in CC398 over time. We identified distinct
human- and livestock-associated CC398 clades and observed
multiple transmissions of CC398 from livestock to humans and
between countries, lending quantitative support to previous
reports. Of note, we identified a subclade within the
livestock-associated clade comprised of isolates from hospital
environments and newborn babies, suggesting that
livestock-associated CC398 is capable of onward transmission in
hospitals. In addition, our analysis revealed significant
differences in the dynamics of resistance to methicillin and
tetracycline related to contrasting historical patterns of
antibiotic usage between the livestock industry and human
medicine. We also identified significant differences in patterns
of gain and loss of different tetracycline resistance
determinants, which we ascribe to epistatic interactions between
the resistance genes and/or differences in the modes of
inheritance of the resistance determinants.",
journal = "Appl. Environ. Microbiol.",
volume = 80,
number = 23,
pages = "7275--7282",
month = dec,
year = 2014,
keywords = "
antibiotics;Staphylococcus;Staph\_evolutionary\_history;bacterial
comparative
genomics;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
}
@ARTICLE{Stinear2014-ay,
title = "Adaptive Change Inferred from Genomic Population Analysis of the
{ST93} Epidemic Clone of {Community-Associated} Methicillin
Resistant Staphylococcus aureus",
author = "Stinear, Timothy P. and Holt, Kathryn E. and Chua, Kyra and
Stepnell, Justin and Tuck, Kellie L. and Coombs, Geoffrey and
Harrison, Paul Francis and Seemann, Torsten and Howden, Benjamin
P.",
abstract = "Community associated methicillin resistant Staphylococcus aureus
(CA-MRSA) has emerged as a major public health problem around the
world. In Australia, ST93-IV[2B] is the dominant CA-MRSA clone
and displays significantly greater virulence than other S.
aureus. Here we have examined the evolution of ST93 via genomic
analysis of 12 MSSA and 44 MRSA ST93 isolates, collected from
around Australia over a 17-year period. Comparative analysis
revealed a core genome of 2.6 Mb, sharing greater than 99.7\%
nucleotide identity. The accessory genome was 0.45 Mb and
comprised additional mobile DNA elements, harboring resistance to
erythromycin, trimethoprim and tetracycline. Phylogenetic
inference revealed a molecular clock and suggested that a single
clone of methicillin susceptible, Panton-Valentine leukocidin
(PVL) positive, ST93 S. aureus likely spread from North Western
Australia in the early 1970s, acquiring methicillin resistance at
least twice in the mid 1990s. We also explored associations
between genotype and important MRSA phenotypes including
oxacillin MIC and production of exotoxins ($\alpha$-hemolysin,
$\delta$-hemolysin, PSM$\alpha$3, and PVL). High-level expression
of $\alpha$-hemolysin is a signature feature of ST93 and reduced
expression in eight isolates was readily explained by mutations
in the agr locus. However, subtle but significant decreases in
$\delta$-hemolysin were also noted over time that coincided with
decreasing oxacillin resistance and were independent of agr
mutations. The evolution of ST93 S. aureus is thus associated
with a reduction in both exotoxin expression and oxacillin MIC,
suggesting MRSA ST93 isolates are under pressure for adaptive
change.",
journal = "Genome Biol. Evol.",
month = jan,
year = 2014,
keywords = "
Staphylococcus;antibiotics;oxacillin;Staph\_evolutionary\_history;bacterial
comparative
genomics;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Paterson2015-nr,
title = "Capturing the cloud of diversity reveals complexity and
heterogeneity of {MRSA} carriage, infection and transmission",
author = "Paterson, Gavin K and Harrison, Ewan M and Murray, Gemma G R and
Welch, John J and Warland, James H and Holden, Matthew T G and
Morgan, Fiona J E and Ba, Xiaoliang and Koop, Gerrit and Harris,
Simon R and Maskell, Duncan J and Peacock, Sharon J and Herrtage,
Michael E and Parkhill, Julian and Holmes, Mark A",
abstract = "Genome sequencing is revolutionizing clinical microbiology and
our understanding of infectious diseases. Previous studies have
largely relied on the sequencing of a single isolate from each
individual. However, it is not clear what degree of bacterial
diversity exists within, and is transmitted between individuals.
Understanding this 'cloud of diversity' is key to accurate
identification of transmission pathways. Here, we report the deep
sequencing of methicillin-resistant Staphylococcus aureus among
staff and animal patients involved in a transmission network at a
veterinary hospital. We demonstrate considerable within-host
diversity and that within-host diversity may rise and fall over
time. Isolates from invasive disease contained multiple mutations
in the same genes, including inactivation of a global regulator
of virulence and changes in phage copy number. This study
highlights the need for sequencing of multiple isolates from
individuals to gain an accurate picture of transmission networks
and to further understand the basis of pathogenesis.",
journal = "Nat. Commun.",
volume = 6,
pages = "6560",
year = 2015,
keywords = "Staphylococcus;colonization;evolution;phage;bacterial comparative
genomics;Staph\_evolutionary\_history/staph microbial
interactions;Staph\_evolutionary\_history;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
}
@ARTICLE{Moon2015-ue,
title = "Phage-mediated horizontal transfer of a Staphylococcus aureus
virulence-associated genomic island",
author = "Moon, Bo Youn and Park, Joo Youn and Hwang, Sun Yung and
Robinson, D Ashley and Thomas, Jonathan C and Fitzgerald, J Ross
and Park, Yong Ho and Seo, Keun Seok",
abstract = "Staphylococcus aureus is a major pathogen of humans and animals.
The capacity of S. aureus to adapt to different host species and
tissue types is strongly influenced by the acquisition of mobile
genetic elements encoding determinants involved in niche
adaptation. The genomic islands $\nu$Sa$\alpha$ and
$\nu$Sa$\beta$ are found in almost all S. aureus strains and are
characterized by extensive variation in virulence gene content.
However the basis for the diversity and the mechanism underlying
mobilization of the genomic islands between strains are
unexplained. Here, we demonstrated that the genomic island,
$\nu$Sa$\beta$, encoding an array of virulence factors including
staphylococcal superantigens, proteases, and leukotoxins, in
addition to bacteriocins, was transferrable in vitro to human and
animal strains of multiple S. aureus clones via a resident
prophage. The transfer of the $\nu$Sa$\beta$ appears to have been
accomplished by multiple conversions of transducing phage
particles carrying overlapping segments of the $\nu$Sa$\beta$.
Our findings solve a long-standing mystery regarding the
diversification and spread of the genomic island $\nu$Sa$\beta$,
highlighting the central role of bacteriophages in the pathogenic
evolution of S. aureus.",
journal = "Sci. Rep.",
volume = 5,
pages = "9784",
month = apr,
year = 2015,
keywords = "Staphylococcus;plasmid;phage;Staph\_evolutionary\_history;Read-lab-shared;MRSA-VRSA-gene\_transfer;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Hsu2015-dp,
title = "Evolutionary dynamics of methicillin-resistant Staphylococcus
aureus within a healthcare system",
author = "Hsu, Li-Yang and Harris, Simon R and Chlebowicz, Monika A and
Lindsay, Jodi A and Koh, Tse-Hsien and Krishnan, Prabha and Tan,
Thean-Yen and Hon, Pei-Yun and Grubb, Warren B and Bentley,
Stephen D and Parkhill, Julian and Peacock, Sharon J and Holden,
Matthew Tg",
abstract = "BACKGROUND: In the past decade, several countries have seen
gradual replacement of endemic multi-resistant
healthcare-associated methicillin-resistant Staphylococcus aureus
(MRSA) with clones that are more susceptible to antibiotic
treatment. One example is Singapore, where MRSA ST239, the
dominant clone since molecular profiling of MRSA began in the
mid-1980s, has been replaced by ST22 isolates belonging to
EMRSA-15, a recently emerged pandemic lineage originating from
Europe. RESULTS: We investigated the population structure of MRSA
in Singaporean hospitals spanning three decades, using whole
genome sequencing. Applying Bayesian phylogenetic methods we
report that prior to the introduction of ST22, the ST239 MRSA
population in Singapore originated from multiple introductions
from the surrounding region; it was frequently transferred within
the healthcare system resulting in a heterogeneous hospital
population. Following the introduction of ST22 around the
beginning of the millennium, this clone spread rapidly through
Singaporean hospitals, supplanting the endemic ST239 population.
Coalescent analysis revealed that although the genetic diversity
of ST239 initially decreased as ST22 became more dominant, from
2007 onwards the genetic diversity of ST239 began to increase
once more, which was not associated with the emergence of a
sub-clone of ST239. Comparative genomic analysis of the accessory
genome of the extant ST239 population identified that the
Arginine Catabolic Mobile Element arose multiple times, thereby
introducing genes associated with enhanced skin colonization into
this population. CONCLUSIONS: Our results clearly demonstrate
that, alongside clinical practice and antibiotic usage,
competition between clones also has an important role in driving
the evolution of nosocomial pathogen populations.",
journal = "Genome Biol.",
volume = 16,
number = 1,
pages = "81",
month = apr,
year = 2015,
keywords = "Staphylococcus;evolution;bacterial comparative
genomics;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Hau2017-mi,
title = "Draft Genome Sequences of 50 {Methicillin-Resistant}
Staphylococcus aureus Sequence Type 5 Isolates Obtained from a
{U.S}. Hospital",
author = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and
Nicholson, Tracy L",
abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) can be a
commensal or pathogen in humans. Pathogenicity and disease are
related to the acquisition of mobile genetic elements encoding
virulence and antimicrobial resistance genes. Here, we report
draft genome sequences for 50 clinical MRSA isolates from humans
with MRSA-related disease.",
journal = "Genome Announc.",
volume = 5,
number = 44,
month = nov,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Guinane2010-pb,
title = "Evolutionary genomics of Staphylococcus aureus reveals insights
into the origin and molecular basis of ruminant host adaptation",
author = "Guinane, Caitriona M and Ben Zakour, Nouri L and Tormo-Mas, Maria
A and Weinert, Lucy A and Lowder, Bethan V and Cartwright, Robyn
A and Smyth, Davida S and Smyth, Cyril J and Lindsay, Jodi A and
Gould, Katherine A and Witney, Adam and Hinds, Jason and
Bollback, Jonathan P and Rambaut, Andrew and Penad{\'e}s,
Jos{\'e} R and Fitzgerald, J Ross",
abstract = "Phenotypic biotyping has traditionally been used to differentiate
bacteria occupying distinct ecological niches such as host
species. For example, the capacity of Staphylococcus aureus from
sheep to coagulate ruminant plasma, reported over 60 years ago,
led to the description of small ruminant and bovine S. aureus
ecovars. The great majority of small ruminant isolates are
represented by a single, widespread clonal complex (CC133) of S.
aureus, but its evolutionary origin and the molecular basis for
its host tropism remain unknown. Here, we provide evidence that
the CC133 clone evolved as the result of a human to ruminant host
jump followed by adaptive genome diversification. Comparative
whole-genome sequencing revealed molecular evidence for host
adaptation including gene decay and diversification of proteins
involved in host-pathogen interactions. Importantly, several
novel mobile genetic elements encoding virulence proteins with
attenuated or enhanced activity in ruminants were widely
distributed in CC133 isolates, suggesting a key role in its
host-specific interactions. To investigate this further, we
examined the activity of a novel staphylococcal pathogenicity
island (SaPIov2) found in the great majority of CC133 isolates
which encodes a variant of the chromosomally encoded von
Willebrand-binding protein (vWbp(Sov2)), previously demonstrated
to have coagulase activity for human plasma. Remarkably, we
discovered that SaPIov2 confers the ability to coagulate ruminant
plasma suggesting an important role in ruminant disease
pathogenesis and revealing the origin of a defining phenotype of
the classical S. aureus biotyping scheme. Taken together, these
data provide broad new insights into the origin and molecular
basis of S. aureus ruminant host specificity.",
journal = "Genome Biol. Evol.",
volume = 2,
pages = "454--466",
month = jul,
year = 2010,
keywords = "Staphylococcus;colonization;host-pathogen;bacterial comparative
genomics;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
}
@ARTICLE{Kuroda2001-wn,
title = "Whole genome sequencing of meticillin-resistant Staphylococcus
aureus",
author = "Kuroda, M and Ohta, T and Uchiyama, I and Baba, T and Yuzawa, H
and Kobayashi, I and Cui, L and Oguchi, A and Aoki, K and Nagai,
Y and Lian, J and Ito, T and Kanamori, M and Matsumaru, H and
Maruyama, A and Murakami, H and Hosoyama, A and Mizutani-Ui, Y
and Takahashi, N K and Sawano, T and Inoue, R and Kaito, C and
Sekimizu, K and Hirakawa, H and Kuhara, S and Goto, S and
Yabuzaki, J and Kanehisa, M and Yamashita, A and Oshima, K and
Furuya, K and Yoshino, C and Shiba, T and Hattori, M and
Ogasawara, N and Hayashi, H and Hiramatsu, K",
abstract = "BACKGROUND: Staphylococcus aureus is one of the major causes of
community-acquired and hospital-acquired infections. It produces
numerous toxins including superantigens that cause unique disease
entities such as toxic-shock syndrome and staphylococcal scarlet
fever, and has acquired resistance to practically all
antibiotics. Whole genome analysis is a necessary step towards
future development of countermeasures against this organism.
METHODS: Whole genome sequences of two related S aureus strains
(N315 and Mu50) were determined by shot-gun random sequencing.
N315 is a meticillin-resistant S aureus (MRSA) strain isolated in
1982, and Mu50 is an MRSA strain with vancomycin resistance
isolated in 1997. The open reading frames were identified by use
of GAMBLER and GLIMMER programs, and annotation of each was done
with a BLAST homology search, motif analysis, and protein
localisation prediction. FINDINGS: The Staphylococcus genome was
composed of a complex mixture of genes, many of which seem to
have been acquired by lateral gene transfer. Most of the
antibiotic resistance genes were carried either by plasmids or by
mobile genetic elements including a unique resistance island.
Three classes of new pathogenicity islands were identified in the
genome: a toxic-shock-syndrome toxin island family, exotoxin
islands, and enterotoxin islands. In the latter two pathogenicity
islands, clusters of exotoxin and enterotoxin genes were found
closely linked with other gene clusters encoding putative
pathogenic factors. The analysis also identified 70 candidates
for new virulence factors. INTERPRETATION: The remarkable ability
of S aureus to acquire useful genes from various organisms was
revealed through the observation of genome complexity and
evidence of lateral gene transfer. Repeated duplication of genes
encoding superantigens explains why S aureus is capable of
infecting humans of diverse genetic backgrounds, eliciting severe
immune reactions. Investigation of many newly identified gene
products, including the 70 putative virulence factors, will
greatly improve our understanding of the biology of staphylococci
and the processes of infectious diseases caused by S aureus.",
journal = "Lancet",
volume = 357,
number = 9264,
pages = "1225--1240",
month = apr,
year = 2001,
keywords = "antibiotics;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Roach2015-ns,
title = "A Year of Infection in the Intensive Care Unit: Prospective Whole
Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic
Transmissions and Novel Microbiota",
author = "Roach, David J and Burton, Joshua N and Lee, Choli and
Stackhouse, Bethany and Butler-Wu, Susan M and Cookson, Brad T
and Shendure, Jay and Salipante, Stephen J",
abstract = "Bacterial whole genome sequencing holds promise as a disruptive
technology in clinical microbiology, but it has not yet been
applied systematically or comprehensively within a clinical
context. Here, over the course of one year, we performed
prospective collection and whole genome sequencing of nearly all
bacterial isolates obtained from a tertiary care hospital's
intensive care units (ICUs). This unbiased collection of 1,229
bacterial genomes from 391 patients enables detailed exploration
of several features of clinical pathogens. A sizable fraction of
isolates identified as clinically relevant corresponded to
previously undescribed species: 12\% of isolates assigned a
species-level classification by conventional methods actually
qualified as distinct, novel genomospecies on the basis of
genomic similarity. Pan-genome analysis of the most frequently
encountered pathogens in the collection revealed substantial
variation in pan-genome size (1,420 to 20,432 genes) and the rate
of gene discovery (1 to 152 genes per isolate sequenced).
Surprisingly, although potential nosocomial transmission of
actively surveilled pathogens was rare, 8.7\% of isolates
belonged to genomically related clonal lineages that were present
among multiple patients, usually with overlapping hospital
admissions, and were associated with clinically significant
infection in 62\% of patients from which they were recovered.
Multi-patient clonal lineages were particularly evident in the
neonatal care unit, where seven separate Staphylococcus
epidermidis clonal lineages were identified, including one
lineage associated with bacteremia in 5/9 neonates. Our study
highlights key differences in the information made available by
conventional microbiological practices versus whole genome
sequencing, and motivates the further integration of microbial
genome sequencing into routine clinical care.",
journal = "PLoS Genet.",
volume = 11,
number = 7,
pages = "e1005413",
month = jul,
year = 2015,
keywords = "Staphylococcus;pangenome;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Burd2014-nc,
title = "Development of oxacillin resistance in a patient with recurrent
Staphylococcus aureus bacteremia",
author = "Burd, Eileen M and Alam, Mohammad Tauqeer and Passalacqua, Karla
D and Kalokhe, Ameeta S and Eaton, Molly E and Satola, Sarah W
and Kraft, Colleen S and Read, Timothy D",
abstract = "Whole-genome sequencing was used to compare longitudinal
isolates of Staphylococcus aureus that developed resistance to
oxacillin (MIC up to 16 $\mu$g/ml). The mecA gene was absent. A
novel 5-bp TATCC frameshift insertion in a gene encoding an ABC
transporter similar to that of the teichoic acid translocation
ATP-binding protein TagH and a 3-bp GCT nonframeshift insertion
in the pdhA pyruvate dehydrogenase gene were detected in the
oxacillin-resistant isolates.",
journal = "J. Clin. Microbiol.",
publisher = "American Society for Microbiology",
volume = 52,
number = 8,
pages = "3114--3117",
month = aug,
year = 2014,
keywords = "oxacillin;antibiotics;Staphylococcus;My
Publications;My\_Peer\_reviewed;Staphylococcus\_aureus\_genome\_papers"
}
% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Alam2014-fv,
title = "Dissecting vancomycin-intermediate resistance in Staphylococcus
aureus using genome-wide association",
author = "Alam, Md Tauqeer and Petit, 3rd, Robert A and Crispelll, 3rd,
Emily K and Thornton, Timothy A and Conneely, Karen N and Jiang,
Yunxuan and Satola, Sarah W and Read, Timothy D",
abstract = "Vancomycin-intermediate Staphylococcus aureus (VISA) is
currently defined as having minimal inhibitory concentration
(MIC) of 4-8 µg/ml. VISA evolves through changes in multiple
genetic loci with at least 16 candidate genes identified in
clinical and in vitro-selected VISA strains. We report a
whole-genome comparative analysis of 49 vancomycin-sensitive S.
aureus and 26 VISA strains. Resistance to vancomycin was
determined by broth microdilution, Etest, and population
analysis profile-area under the curve (PAP-AUC). Genome-wide
association studies (GWAS) of 55,977 single-nucleotide
polymorphisms identified in one or more strains found one highly
significant association (P = 8.78 E-08) between a nonsynonymous
mutation at codon 481 (H481) of the rpoB gene and increased
vancomycin MIC. Additionally, we used a database of public S.
aureus genome sequences to identify rare mutations in candidate
genes associated with VISA. On the basis of these data, we
proposed a preliminary model called ECM+RMCG for the VISA
phenotype as a benchmark for future efforts. The model predicted
VISA based on the presence of a rare mutation in a set of
candidate genes (walKR, vraSR, graSR, and agrA) and/or three
previously experimentally verified mutations (including the rpoB
H481 locus) with an accuracy of 81\% and a sensitivity of 73\%.
Further, the level of resistance measured by both Etest and
PAP-AUC regressed positively with the number of mutations
present in a strain. This study demonstrated 1) the power of
GWAS for identifying common genetic variants associated with
antibiotic resistance in bacteria and 2) that rare mutations in
candidate gene, identified using large genomic data sets, can
also be associated with resistance phenotypes.",
journal = "Genome Biol. Evol.",
publisher = "Oxford University Press",
volume = 6,
number = 5,
pages = "1174--1185",
month = apr,
year = 2014,
keywords = "bacteria; genomics; phylogeny; whole-genome
sequencing;Staphylococcus;confirmed\_SA-resistance-mutation;My
Publications;antibiotcs-evolution-fitness;My\_Peer\_reviewed;Staphylococcus\_aureus\_genome\_papers;GWAS-bacteria"
}
@ARTICLE{Laabei2014-tg,
title = "Predicting the virulence of {MRSA} from its genome sequence",
author = "Laabei, Maisem and Recker, Mario and Rudkin, Justine K and
Aldeljawi, Mona and Gulay, Zeynep and Sloan, Tim J and Williams,
Paul and Endres, Jennifer L and Bayles, Kenneth W and Fey, Paul
D and Yajjala, Vijaya Kumar and Widhelm, Todd and Hawkins, Erica
and Lewis, Katie and Parfett, Sara and Scowen, Lucy and Peacock,
Sharon J and Holden, Matthew and Wilson, Daniel and Read,
Timothy D and van den Elsen, Jean and Priest, Nicholas K and
Feil, Edward J and Hurst, Laurence D and Josefsson, Elisabet and
Massey, Ruth C",
abstract = "Microbial virulence is a complex and often multifactorial
phenotype, intricately linked to a pathogen's evolutionary
trajectory. Toxicity, the ability to destroy host cell
membranes, and adhesion, the ability to adhere to human tissues,
are the major virulence factors of many bacterial pathogens,
including Staphylococcus aureus. Here, we assayed the toxicity
and adhesiveness of 90 MRSA (methicillin resistant S. aureus)
isolates and found that while there was remarkably little
variation in adhesion, toxicity varied by over an order of
magnitude between isolates, suggesting different evolutionary
selection pressures acting on these two traits. We performed a
genome-wide association study (GWAS) and identified a large
number of loci, as well as a putative network of epistatically
interacting loci, that significantly associated with toxicity.
Despite this apparent complexity in toxicity regulation, a
predictive model based on a set of significant single nucleotide
polymorphisms (SNPs) and insertion and deletions events (indels)
showed a high degree of accuracy in predicting an isolate's
toxicity solely from the genetic signature at these sites. Our
results thus highlight the potential of using sequence data to
determine clinically relevant parameters and have further
implications for understanding the microbial virulence of this
opportunistic pathogen.",
journal = "Genome Res.",
publisher = "Cold Spring Harbor Lab",
volume = 24,
number = 5,
pages = "839--849",
month = may,
year = 2014,
keywords = "bacerial\_genetics;Staphylococcus;toxicity;My
Publications;My\_Peer\_reviewed;Read-lab-shared;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers;GWAS-bacteria;Staph\_evolution\_toxins"
}
@ARTICLE{Passalacqua2012-yq,
title = "A mutation in the {PP2C} phosphatase gene in a Staphylococcus
aureus {USA300} clinical isolate with reduced susceptibility to
vancomycin and daptomycin",
author = "Passalacqua, Karla D and Satola, Sarah W and Crispell, Emily K
and Read, Timothy D",
journal = "Antimicrob. Agents Chemother.",
publisher = "American Society for Microbiology",
volume = 56,
number = 10,
pages = "5212--5223",
year = 2012,
keywords = "Staphylococcus;My
Publications;imported\_from\_papers\_14Nov2013;My\_Peer\_reviewed;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Nubel2010-gs,
title = "A timescale for evolution, population expansion, and spatial
spread of an emerging clone of methicillin-resistant
Staphylococcus aureus",
author = "N{\"u}bel, Ulrich and Dordel, Janina and Kurt, Kevin and
Strommenger, Birgit and Westh, Henrik and Shukla, Sanjay K and
Zemlickov{\'a}, Helena and Leblois, Rapha{\"e}l and Wirth,
Thierry and Jombart, Thibaut and Balloux, Fran{\c c}ois and
Witte, Wolfgang",
abstract = "Due to the lack of fossil evidence, the timescales of bacterial
evolution are largely unknown. The speed with which genetic
change accumulates in populations of pathogenic bacteria,
however, is a key parameter that is crucial for understanding the
emergence of traits such as increased virulence or antibiotic
resistance, together with the forces driving pathogen spread.
Methicillin-resistant Staphylococcus aureus (MRSA) is a common
cause of hospital-acquired infections. We have investigated an
MRSA strain (ST225) that is highly prevalent in hospitals in
Central Europe. By using mutation discovery at 269 genetic loci
(118,804 basepairs) within an international isolate collection,
we ascertained extremely low diversity among European ST225
isolates, indicating that a recent population bottleneck had
preceded the expansion of this clone. In contrast, US isolates
were more divergent, suggesting they represent the ancestral
population. While diversity was low, however, our results
demonstrate that the short-term evolutionary rate in this natural
population of MRSA resulted in the accumulation of measurable DNA
sequence variation within two decades, which we could exploit to
reconstruct its recent demographic history and the spatiotemporal
dynamics of spread. By applying Bayesian coalescent methods on
DNA sequences serially sampled through time, we estimated that
ST225 had diverged since approximately 1990 (1987 to 1994), and
that expansion of the European clade began in 1995 (1991 to
1999), several years before the new clone was recognized.
Demographic analysis based on DNA sequence variation indicated a
sharp increase of bacterial population size from 2001 to 2004,
which is concordant with the reported prevalence of this strain
in several European countries. A detailed ancestry-based
reconstruction of the spatiotemporal dispersal dynamics suggested
a pattern of frequent transmission of the ST225 clone among
hospitals within Central Europe. In addition, comparative
genomics indicated complex bacteriophage dynamics.",
journal = "PLoS Pathog.",
volume = 6,
number = 4,
pages = "e1000855",
month = apr,
year = 2010,
keywords = "Staphylococcus;evolution;bacterial comparative
genomics;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Harris2013-mf,
title = "Whole-genome sequencing for analysis of an outbreak of
meticillin-resistant Staphylococcus aureus: a descriptive study",
author = "Harris, Simon R and Cartwright, Edward J P and T{\"o}r{\"o}k, M
Est{\'e}e and Holden, Matthew T G and Brown, Nicholas M and
Ogilvy-Stuart, Amanda L and Ellington, Matthew J and Quail,
Michael A and Bentley, Stephen D and Parkhill, Julian and
Peacock, Sharon J",
abstract = "BACKGROUND: The emergence of meticillin-resistant Staphylococcus
aureus (MRSA) that can persist in the community and replace
existing hospital-adapted lineages of MRSA means that it is
necessary to understand transmission dynamics in terms of
hospitals and the community as one entity. We assessed the use
of whole-genome sequencing to enhance detection of MRSA
transmission between these settings. METHODS: We studied a
putative MRSA outbreak on a special care baby unit (SCBU) at a
National Health Service Foundation Trust in Cambridge, UK. We
used whole-genome sequencing to validate and expand findings
from an infection-control team who assessed the outbreak through
conventional analysis of epidemiological data and antibiogram
profiles. We sequenced isolates from all colonised patients in
the SCBU, and sequenced MRSA isolates from patients in the
hospital or community with the same antibiotic susceptibility
profile as the outbreak strain. FINDINGS: The hospital
infection-control team identified 12 infants colonised with MRSA
in a 6 month period in 2011, who were suspected of being linked,
but a persistent outbreak could not be confirmed with
conventional methods. With whole-genome sequencing, we
identified 26 related cases of MRSA carriage, and showed
transmission occurred within the SCBU, between mothers on a
postnatal ward, and in the community. The outbreak MRSA type was
a new sequence type (ST) 2371, which is closely related to ST22,
but contains genes encoding Panton-Valentine leucocidin.
Whole-genome sequencing data were used to propose and confirm
that MRSA carriage by a staff member had allowed the outbreak to
persist during periods without known infection on the SCBU and
after a deep clean. INTERPRETATION: Whole-genome sequencing
holds great promise for rapid, accurate, and comprehensive
identification of bacterial transmission pathways in hospital
and community settings, with concomitant reductions in
infections, morbidity, and costs. FUNDING: UK Clinical Research
Collaboration Translational Infection Research Initiative,
Wellcome Trust, Health Protection Agency, and the National
Institute for Health Research Cambridge Biomedical Research
Centre.",
journal = "Lancet Infect. Dis.",
publisher = "Elsevier",
volume = 13,
number = 2,
pages = "130--136",
month = feb,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Stegger2012-hy,
title = "Genome sequence of Staphylococcus aureus strain 11819-97, an
{ST80-IV} European community-acquired methicillin-resistant
isolate",
author = "Stegger, Marc and Price, Lance B and Larsen, Anders R and
Gillece, John D and Waters, Andrew E and Skov, Robert and
Andersen, Paal S",
abstract = "The European methicillin-resistant Staphylococcus aureus (MRSA)
clone ST80-IV has historically dominated community-associated
infections in major parts of Europe and is a lineage strongly
linked to skin and soft tissue infections. Here, we report the
genome sequence of an ST80-IV representative, 11819-97, isolated
from a skin infection in Denmark in 1997.",
journal = "J. Bacteriol.",
publisher = "Am Soc Microbiol",
volume = 194,
number = 6,
pages = "1625--1626",
month = mar,
year = 2012,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Treangen2014-oh,
title = "Complete Genome Sequence of the Quality Control Strain
Staphylococcus aureus subsp. aureus {ATCC} 25923",
author = "Treangen, Todd J and Maybank, Rosslyn A and Enke, Sana and
Friss, Mary Beth and Diviak, Lynn F and Karaolis, David K R and
Koren, Sergey and Ondov, Brian and Phillippy, Adam M and
Bergman, Nicholas H and Rosovitz, M J",
abstract = "Staphylococcus aureus subsp. aureus ATCC 25923 is commonly used
as a control strain for susceptibility testing to antibiotics
and as a quality control strain for commercial products. We
present the completed genome sequence for the strain, consisting
of the chromosome and a 27.5-kb plasmid.",
journal = "Genome Announc.",
publisher = "Am Soc Microbiol",
volume = 2,
number = 6,
month = nov,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Price2014-jt,
title = "Whole-genome sequencing shows that patient-to-patient
transmission rarely accounts for acquisition of Staphylococcus
aureus in an intensive care unit",
author = "Price, James R and Golubchik, Tanya and Cole, Kevin and Wilson,
Daniel J and Crook, Derrick W and Thwaites, Guy E and Bowden,
Rory and Walker, A Sarah and Peto, Timothy E A and Paul, John
and Llewelyn, Martin J",
abstract = "BACKGROUND: Strategies to prevent Staphylococcus aureus
infection in hospitals focus on patient-to-patient transmission.
We used whole-genome sequencing to investigate the role of
colonized patients as the source of new S. aureus acquisitions,
and the reliability of identifying patient-to-patient
transmission using the conventional approach of spa typing and
overlapping patient stay. METHODS: Over 14 months, all
unselected patients admitted to an adult intensive care unit
(ICU) were serially screened for S. aureus. All available
isolates (n = 275) were spa typed and underwent whole-genome
sequencing to investigate their relatedness at high resolution.
RESULTS: Staphylococcus aureus was carried by 185 of 1109
patients sampled within 24 hours of ICU admission (16.7\%); 59
(5.3\%) patients carried methicillin-resistant S. aureus (MRSA).
Forty-four S. aureus (22 MRSA) acquisitions while on ICU were
detected. Isolates were available for genetic analysis from 37
acquisitions. Whole-genome sequencing indicated that 7 of these
37 (18.9\%) were transmissions from other colonized patients.
Conventional methods (spa typing combined with overlapping
patient stay) falsely identified 3 patient-to-patient
transmissions (all MRSA) and failed to detect 2 acquisitions and
4 transmissions (2 MRSA). CONCLUSIONS: Only a minority of S.
aureus acquisitions can be explained by patient-to-patient
transmission. Whole-genome sequencing provides the resolution to
disprove transmission events indicated by conventional methods
and also to reveal otherwise unsuspected transmission events.
Whole-genome sequencing should replace conventional methods for
detection of nosocomial S. aureus transmission.",
journal = "Clin. Infect. Dis.",
publisher = "cid.oxfordjournals.org",
volume = 58,
number = 5,
pages = "609--618",
month = mar,
year = 2014,
keywords = "Staphylococcus aureus transmission; adult; intensive care unit;
spa typing; whole-genome
sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Sass2012-jk,
title = "Genome sequence of Staphylococcus aureus {VC40}, a
vancomycin-and daptomycin-resistant strain, to study the
genetics of development of resistance to currently applied
last-resort antibiotics",
author = "Sass, Peter and Berscheid, Anne and Jansen, Andrea and
Oedenkoven, Marion and Szekat, Christiane and Strittmatter, Axel
and Gottschalk, Gerhard and Bierbaum, Gabriele",
abstract = "ABSTRACT The increasing emergence of multidrug-resistant
Staphylococcus aureus is a problem of global importance. Here,
we report the genome of S. aureus VC40, which is resistant to
the last-resort antibiotics vancomycin and daptomycin. Its
genome sequence ...",
journal = "J. Bacteriol.",
publisher = "Am Soc Microbiol",
volume = 194,
number = 8,
pages = "2107--2108",
year = 2012,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Ip2014-mq,
title = "Draft Genome Sequence of {Methicillin-Resistant} Staphylococcus
aureus {CUHK\_188} ({ST188)}, a Health {Care-Associated}
Bacteremic Isolate from Hong Kong",
author = "Ip, Margaret and Wang, Zheng and Lam, Wai Yip and Zhou, Haokui
and Tsui, Stephen",
abstract = "We report the draft genome sequence of a methicillin-resistant
Staphylococcus aureus strain designated CUHK\_188, isolated from
a bacteremic patient undergoing treatment at a university
teaching hospital in Hong Kong. This strain belongs to sequence
type 188 (ST188), with spa type t189 and staphylococcal cassette
chromosome mec type V.",
journal = "Genome Announc.",
publisher = "Am Soc Microbiol",
volume = 2,
number = 2,
month = apr,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Huang2012-zq,
title = "Complete genome sequence of Staphylococcus aureus M013, a
pvl-positive, {ST59-SCCmec} type {V} strain isolated in Taiwan",
author = "Huang, Tzu-Wen and Chen, Feng-Jui and Miu, Wei-Chieh and Liao,
Tsai-Lien and Lin, Ann-Chi and Huang, I-Wen and Wu, Keh-Ming and
Tsai, Shih-Feng and Chen, Ying-Tsong and Lauderdale, Tsai-Ling
Yang",
abstract = "We report the complete genome sequence of M013, a representative
strain of a pvl-positive, sequence type 59-staphylococcal
cassette chromosome mec type V (ST59-SCCmec type V)
community-associated methicillin-resistant Staphylococcus aureus
(CA-MRSA) clone in Taiwan. Comparison of M013 with the genomes
of two CA-MRSA strains in the United States revealed major
differences in the regions covering several genomic islands and
prophages.",
journal = "J. Bacteriol.",
publisher = "Am Soc Microbiol",
volume = 194,
number = 5,
pages = "1256--1257",
month = mar,
year = 2012,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Bouchard2012-ud,
title = "Genome sequence of Staphylococcus aureus Newbould 305, a strain
associated with mild bovine mastitis",
author = "Bouchard, Damien and Peton, Vincent and Almeida, Sintia and Le
Mar{\'e}chal, Caroline and Miyoshi, Anderson and Azevedo, Vasco
and Berkova, Nadia and Rault, Lucie and Fran{\c c}ois, Patrice
and Schrenzel, Jacques and Even, Sergine and Hernandez, David
and Le Loir, Yves",
abstract = "Staphylococcus aureus is a major etiological agent of mastitis
in ruminants. We report here the genome sequence of bovine
strain Newbould 305, isolated in the 1950s in a case of bovine
mastitis and now used as a model strain able to reproducibly
induce chronic mastitis in cows.",
journal = "J. Bacteriol.",
publisher = "Am Soc Microbiol",
volume = 194,
number = 22,
pages = "6292--6293",
month = nov,
year = 2012,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Schijffelen2013-dh,
title = "Whole genome analysis of epidemiologically closely related
Staphylococcus aureus isolates",
author = "Schijffelen, Maarten and Konstantinov, Sergey R and Lina,
G{\'e}rard and Spiliopoulou, Iris and van Duijkeren, Engeline
and Brouwer, Ellen C and Fluit, Ad C",
abstract = "The change of the bacteria from colonizers to pathogens is
accompanied by a drastic change in expression profiles. These
changes may be due to environmental signals or to mutational
changes. We therefore compared the whole genome sequences of
four sets of S. aureus isolates. Three sets were from the same
patients. The isolates of each pair (S1800/S1805, S2396/S2395,
S2398/S2397, an isolate from colonization and an isolate from
infection, respectively) were obtained within <30 days of each
other and the isolate from infection caused skin infections. The
isolates were then compared for differences in gene content and
SNPs. In addition, a set of isolates from a colonized pig and a
farmer from the same farm at the same time (S0462 and S0460)
were analyzed. The isolates pair S1800/S1805 showed a difference
in a prophage, but these are easily lost or acquired. However,
S1805 contained an integrative conjugative element not present
in S1800. In addition, 92 SNPs were present in a variety of
genes and the isolates S1800 and S1805 were not considered a
pair. Between S2395/S2396 two SNPs were present: one was in an
intergenic region and one was a synonymous mutation in a
putative membrane protein. Between S2397/S2398 only one
synonymous mutation in a putative lipoprotein was found. The two
farm isolates were very similar and showed 12 SNPs in genes that
belong to a number of different functional categories. However,
we cannot pinpoint any gene that explains the change from
carrier status to infection. The data indicate that differences
between the isolate from infection and the colonizing isolate
for S2395/S2396 and S2397/S2398 exist as well as between
isolates from different hosts, but S1800/S1805 are not clonal.",
journal = "PLoS One",
publisher = "dx.plos.org",
volume = 8,
number = 10,
pages = "e78340",
month = oct,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Thomas2012-gq,
title = "Draft genome sequences of Staphylococcus aureus sequence type 34
({ST34}) and {ST42} hybrids",
author = "Thomas, Jonathan C and Godfrey, Paul A and Feldgarden, Michael
and Robinson, D Ashley",
abstract = "Staphylococcus aureus is a major cause of
antimicrobial-resistant infections of humans. Hybrids of S.
aureus, which originate from large-scale chromosomal
recombinations between parents of distinct genetic backgrounds,
are of interest from clinical and evolutionary perspectives. We
present draft genome sequences of two S. aureus hybrids of
sequence type 34 (ST34) and ST42.",
journal = "J. Bacteriol.",
publisher = "Am Soc Microbiol",
volume = 194,
number = 10,
pages = "2740--2741",
month = may,
year = 2012,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Larner-Svensson2013-jf,
title = "Complete Genome Sequence of Staphylococcus aureus Strain M1, a
Unique {t024-ST8-IVa} Danish {Methicillin-Resistant} S. aureus
Clone",
author = "Larner-Svensson, Hanna and Worning, Peder and Bartels, Mette D
and Hestbjerg Hansen, Lars and Boye, Kit and Westh, Henrik",
abstract = "We report the genome sequence, in five contigs, of a
methicillin-resistant Staphylococcus aureus isolate designated
M1. This clinical isolate was from the index patient of a
methicillin-resistant Staphylococcus aureus (MRSA) outbreak in
Copenhagen, Denmark, that started in 2003. This strain is
sequence type 8 (ST8), spa type t024, and staphylococcal
cassette chromosome mec element (SCCmec) type IVa.",
journal = "Genome Announc.",
publisher = "Am Soc Microbiol",
volume = 1,
number = 3,
month = jun,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Prabhakara2013-hi,
title = "Genome sequencing unveils a novel sea enterotoxin-carrying {PVL}
phage in Staphylococcus aureus {ST772} from India",
author = "Prabhakara, Sushma and Khedkar, Supriya and Shambat, Srikanth
Mairpady and Srinivasan, Rajalakshmi and Basu, Atanu and
Norrby-Teglund, Anna and Seshasayee, Aswin Sai Narain and
Arakere, Gayathri",
abstract = "Staphylococcus aureus is a major human pathogen, first
recognized as a leading cause of hospital-acquired infections.
Community-associated S. aureus (CA-SA) pose a greater threat due
to increase in severity of infection and disease among children
and healthy adults. CA-SA strains in India are genetically
diverse, among which is the sequence type (ST) 772, which has
now spread to Australia, Europe and Japan. Towards understanding
the genetic characteristics of ST772, we obtained draft genome
sequences of five relevant clinical isolates and studied the
properties of their PVL-carrying prophages, whose presence is a
defining hallmark of CA-SA. We show that this is a novel
prophage, which carries the structural genes of the hlb-carrying
prophage and includes the sea enterotoxin. This architecture
probably emerged early within the ST772 lineage, at least in
India. The sea gene, unique to ST772 PVL, despite having
promoter sequence characteristics typical of low expression,
appears to be highly expressed during early phase of growth in
laboratory conditions. We speculate that this might be a
consequence of its novel sequence context. The crippled nature
of the hlb-converting prophage in ST772 suggests that widespread
mobility of the sea enterotoxin might be a selective force
behind its 'transfer' to the PVL prophage. Wild type ST772
strains induced strong proliferative responses as well as high
cytotoxic activity against neutrophils, likely mediated by
superantigen SEA and the PVL toxin respectively. Both
proliferation and cytotoxicity were markedly reduced in a cured
ST772 strain indicating the impact of the phage on virulence.
The presence of SEA alongside the genes for the immune
system-modulating PVL toxin may contribute to the success and
virulence of ST772.",
journal = "PLoS One",
publisher = "dx.plos.org",
volume = 8,
number = 3,
pages = "e60013",
month = mar,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Biswas2015-xv,
title = "Draft Genome Sequences of Five Clinical {Methicillin-Resistant}
Staphylococcus aureus Isolates and a {Methicillin-Resistant}
Staphylococcus epidermidis Isolate",
author = "Biswas, Rajesh Kumar and Kock, Marleen M and Adelowotan, Toyin
and Strasheim, Wilhelmina and Mahomed, Tanweer Goolam and
Salawu, Adeola and Ehlers, Marthie M",
abstract = "We report the complete draft genome sequences of five
individually isolated strains of methicillin-resistant
Staphylococcus aureus (MRSA) and a Staphylococcus epidermidis
strain. These clinically important isolates have staphylococcal
cassette chromosome mec type A, while Panton-Valentine
leukocidin (PVL) toxin coding genes were present in MRSA
isolates only.",
journal = "Genome Announc.",
publisher = "Am Soc Microbiol",
volume = 3,
number = 4,
month = jul,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Sassi2014-nj,
title = "Draft Genome Sequence of Staphylococcus aureus subsp. aureus
Strain {HG003}, an {NCTC8325} Derivative",
author = "Sassi, Mohamed and Felden, Brice and Augagneur, Yoann",
abstract = "We report the draft genome sequence of a Staphylococcus aureus
NCTC8325 derivative, strain HG003. HG003 contains functional
global regulators rsbU and tcaR and is therefore considered as a
reference for studies of regulation and virulence. The genome is
composed of 2,797,898 bp and will be essential for subsequent
RNAseq analysis.",
journal = "Genome Announc.",
publisher = "Am Soc Microbiol",
volume = 2,
number = 4,
month = aug,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Daligault2014-kl,
title = "Genome Assembly of {Methicillin-Resistant} Quality Control
Strain Staphylococcus aureus {CDC73-57501} ({ATCC} 29247)",
author = "Daligault, H E and Davenport, K W and Minogue, T D and
Bishop-Lilly, K A and Broomall, S M and Bruce, D C and Chain, P
S and Coyne, S R and Freitas, T and Frey, K G and Gibbons, H S
and Jaissle, J and Lo, C-C and Meincke, L and Munk, A C and
Redden, C L and Rosenzweig, C N and Johnson, S L",
abstract = "Staphylococcus aureus is a major cause of bacterial infections
in the United States, with high percentages of serious
infections resistant to a variety of $\beta$-lactam antibiotics.
Here, we present the scaffolded genome assembly into 16 contigs
of S. aureus CDC73-57501 (ATCC 29247), a methicillin-resistant
quality control strain.",
journal = "Genome Announc.",
publisher = "Am Soc Microbiol",
volume = 2,
number = 5,
month = oct,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Stevens2015-lt,
title = "Complete and Assembled Genome Sequence of Staphylococcus aureus
{RKI4}, a {Food-Poisoning} Strain Exhibiting a Novel S. aureus
Pathogenicity Island Carrying seb",
author = "Stevens, Marc J A and Stephan, Roger and Johler, Sophia",
abstract = "The genome of Staphylococcus aureus RKI4, a strain isolated from
feces of a patient in a case of staphylococcal food poisoning,
was sequenced using combined Illumina and single-molecule
real-time sequencing. Hierarchical assembly of the genome
resulted in a 2,725,654-bp chromosome and a 17,905-bp mobile
genetic element.",
journal = "Genome Announc.",
publisher = "Am Soc Microbiol",
volume = 3,
number = 4,
month = jul,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Harrison2013-vq,
title = "Whole genome sequencing identifies zoonotic transmission of
{MRSA} isolates with the novel mecA homologue mecC",
author = "Harrison, Ewan M and Paterson, Gavin K and Holden, Matthew T G
and Larsen, Jesper and Stegger, Marc and Larsen, Anders Rhod and
Petersen, Andreas and Skov, Robert L and Christensen, Judit
Marta and Bak Zeuthen, Anne and Heltberg, Ole and Harris, Simon
R and Zadoks, Ruth N and Parkhill, Julian and Peacock, Sharon J
and Holmes, Mark A",
abstract = "Several methicillin-resistant Staphylococcus aureus (MRSA)
lineages that carry a novel mecA homologue (mecC) have recently
been described in livestock and humans. In Denmark, two
independent human cases of mecC-MRSA infection have been linked
to a livestock reservoir. We investigated the molecular
epidemiology of the associated MRSA isolates using whole genome
sequencing (WGS). Single nucleotide polymorphisms (SNP) were
defined and compared to a reference genome to place the isolates
into a phylogenetic context. Phylogenetic analysis revealed two
distinct farm-specific clusters comprising isolates from the
human case and their own livestock, whereas human and animal
isolates from the same farm only differed by a small number of
SNPs, which supports the likelihood of zoonotic transmission.
Further analyses identified a number of genes and mutations that
may be associated with host interaction and virulence. This
study demonstrates that mecC-MRSA ST130 isolates are capable of
transmission between animals and humans, and underscores the
potential of WGS in epidemiological investigations and source
tracking of bacterial infections.",
journal = "EMBO Mol. Med.",
publisher = "embomolmed.embopress.org",
volume = 5,
number = 4,
pages = "509--515",
month = apr,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
}
@ARTICLE{Nair2011-sm,
title = "Whole-genome sequencing of Staphylococcus aureus strain
{RN4220}, a key laboratory strain used in virulence research,
identifies mutations that affect not only virulence factors but
also the fitness of the strain",
author = "Nair, Dhanalakshmi and Memmi, Guido and Hernandez, David and
Bard, Jonathan and Beaume, Marie and Gill, Steven and Francois,
Patrice and Cheung, Ambrose L",
abstract = "ABSTRACT Staphylococcus aureus RN4220, a cloning intermediate,
is sometimes used in virulence, resistance, and metabolic
studies. Using whole- genome sequencing, we showed that RN4220
differs from NCTC8325 and contains a number of genetic
polymorphisms ...",
journal = "J. Bacteriol.",
publisher = "Am Soc Microbiol",
volume = 193,
number = 9,
pages = "2332--2335",
year = 2011,
keywords = "Staphylococcus;imported\_from\_papers\_14Nov2013;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Li2011-rd,
title = "Complete genome sequence of Staphylococcus aureus T0131, an
{ST239-MRSA-SCCmec} type {III} clone isolated in China",
author = "Li, Yang and Cao, Boyang and Zhang, Yongfu and Zhou, Jiali and
Yang, Bin and Wang, Lei",
abstract = "We report here the complete genome sequence of Staphylococcus
aureus T0131, which is a multiresistant clinical isolate
recovered in China and the first sequenced epidemic
ST239-MRSA-SCCmec type III strain obtained in Asia. Comparison
with two published genomes of ST239 reveals the polymorphism
among strains of this type from different continents.",
journal = "J. Bacteriol.",
publisher = "Am Soc Microbiol",
volume = 193,
number = 13,
pages = "3411--3412",
month = jul,
year = 2011,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Chen2014-tq,
title = "Reduced susceptibility to vancomycin in isogenic Staphylococcus
aureus strains of sequence type 59: tracking evolution and
identifying mutations by whole-genome sequencing",
author = "Chen, Chih-Jung and Lin, Mei-Hui and Shu, Jwu-Ching and Lu,
Jang-Jih",
abstract = "Objectives Vancomycin-intermediate Staphylococcus aureus (VISA)
and heterogeneous VISA (hVISA) phenotypes are increasingly
reported in methicillin-resistant S. aureus (MRSA) strains of
distinct genetic backgrounds. This study tracked genetic
evolution during the ...",
journal = "J. Antimicrob. Chemother.",
publisher = "Br Soc Antimicrob Chemo",
volume = 69,
number = 2,
pages = "349--354",
year = 2014,
keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Van_Der_Mee-Marquet2013-sr,
title = "Whole-genome sequence of the ancestral animal-borne {ST398}
Staphylococcus aureus strain {S123}",
author = "Van Der Mee-Marquet, Nathalie and Hernandez, David and Bertrand,
Xavier and Quentin, Roland and Corvaglia, Anna-Rita and Fran{\c
c}ois, Patrice",
abstract = "ABSTRACT Sequence type 398 (ST398) Staphylococcus aureus was
originally reported in livestock. We announce the complete
genome sequence of an ST398 methicillin-susceptible S. aureus
strain of animal origin, S123. The genome sequence reveals a
wild-type ...",
journal = "Genome Announc.",
publisher = "Am Soc Microbiol",
volume = 1,
number = 5,
pages = "e00692--13",
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
}
@ARTICLE{Diene2015-nq,
title = "Comparative genomics to investigate the emergence of
community-associated methicillin-resistant Staphylococcus aureus
({CA-MRSA}) {USA300} clone in Geneva, Switzerland",
author = "Diene, S M and Von Dach, E and Fankhauser, C and Bonetti, E-J
and Schrenzel, J and Harbarth, S and Fran{\c c}ois, P",
abstract = "... Comparative genomics to investigate the emergence of
community-associated methicillin-resistant Staphylococcus aureus
(CA-MRSA) USA300 clone in Geneva, Switzerland. ...
Solexa-Illumina was used for whole genome sequencing (WGS) of
all USA300 isolated in 2013. ...",
journal = "Antimicrob. Resist. Infect. Control",
publisher = "BioMed Central",
volume = 4,
number = "Suppl 1",
pages = "P197",
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Castillo-Ramirez2012-to,
title = "Phylogeographic variation in recombination rates within a global
clone of {Methicillin-Resistant} Staphylococcus aureus ({MRSA})",
author = "Castillo-Ram{\'\i}rez, Santiago and Corander, Jukka and
Marttinen, Pekka and Aldeljawi, Mona and Hanage, William P and
Westh, Henrik and Boye, Kit and Gulay, Zeynep and Bentley,
Stephen D and Parkhill, Julian and Holden, Matthew T and Feil,
Edward J",
abstract = "ABSTRACT: BACKGROUND: Next-generation sequencing (NGS) is a
powerful tool for understanding both patterns of descent over
time and space (phylogeography) and the molecular processes
underpinning genome divergence in pathogenic bacteria. Here, we
describe a synthesis between these perspectives by employing a
recently developed Bayesian approach, BRATNextGen, for detecting
recombination on an expanded NGS dataset of the globally
disseminated methicillin-resistant Staphylococcus aureus (MRSA)
clone ST239. RESULTS: The data confirm strong geographical
clustering at continental, national and city scales and
demonstrate that the rate of recombination varies significantly
between phylogeographic sub-groups representing independent
introductions from Europe. These differences are most striking
when mobile non-core genes are included, but remain apparent
even when only considering the stable core genome. The
monophyletic ST239 sub-group corresponding to isolates from
South America shows heightened recombination, the sub-group
predominantly from Asia shows an intermediate level, and a very
low level of recombination is noted in a third sub-group
representing a large collection from Turkey. CONCLUSIONS: We
show that the rapid global dissemination of a single pathogenic
bacterial clone results in local variation in measured
recombination rates. Possible explanatory variables include the
size and time since emergence of each defined sub-population (as
determined by the sampling frame), variation in transmission
dynamics due to host movement, and changes in the bacterial
genome affecting the propensity for recombination.",
journal = "Genome Biol.",
publisher = "biomedcentral.com",
volume = 13,
number = 12,
pages = "R126",
month = dec,
year = 2012,
keywords = "
Staphylococcus;recombination;imported\_from\_papers\_14Nov2013;Staph\_evolutionary\_history;bacterial
comparative genomics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Boyle-Vavra2011-vl,
title = "Comparative genome sequencing of an isogenic pair of {USA800}
clinical methicillin-resistant Staphylococcus aureus isolates
obtained before and after daptomycin treatment failure",
author = "Boyle-Vavra, Susan and Jones, Marcus and Gourley, Brett L and
Holmes, Michael and Ruf, Rebecca and Balsam, Ashley R and
Boulware, David R and Kline, Susan and Jawahir, Selina and
Devries, Aaron and Peterson, Scott N and Daum, Robert S",
abstract = "We describe here a clinical daptomycin treatment failure in a
patient with recurrent methicillin-resistant Staphylococcus
aureus (MRSA) bacteremia in whom daptomycin was administered
after a failed empirical treatment course with vancomycin and
piperacillin-tazobactam. We had the opportunity to compare the
genome sequences of an isogenic pair of daptomycin-susceptible
and -resistant MRSA isolates obtained before and after
initiation of daptomycin therapy, respectively. The genotype of
both isolates was USA800, ST5, SCCmec type IV, agr type II.
There was no increase in cell wall thickness in the
daptomycin-resistant strain despite having decreased
susceptibility to both vancomycin and daptomycin. By comparing
the genome sequences by pyrosequencing, we identified a
polymorphism (S337L) in the tenth transmembrane segment of the
multiple peptide resistance factor, MprF, encoding lysyl
phosphatidylglycerol transferase. This enzyme has been shown
previously to promote repulsion of daptomycin at the cell
surface by addition of positively charged lysine to
phosphatidylglycerol. Also, the hlb open reading frame (ORF)
encoding the $\beta$-toxin was interrupted by a prophage in the
daptomycin-susceptible strain; this phage was missing in the
daptomycin-resistant isolate and the hlb ORF was restored. Loss
of the phage in the resistant isolate also resulted in loss of
the virulence factor genes clpP, scn, and sak. This is the first
study to use pyrosequencing to compare the genomes of a
daptomycin-susceptible/resistant MRSA isolate pair obtained
during failed daptomycin therapy in humans.",
journal = "Antimicrob. Agents Chemother.",
publisher = "Am Soc Microbiol",
volume = 55,
number = 5,
pages = "2018--2025",
month = may,
year = 2011,
keywords = "
Staphylococcus;phage;confirmed\_SA-resistance-mutation;imported\_from\_papers\_14Nov2013;bacterial
comparative genomics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Judge2015-kn,
title = "Early insights into the potential of the Oxford Nanopore {MinION}
for the detection of antimicrobial resistance genes",
author = "Judge, Kim and Harris, Simon R and Reuter, Sandra and Parkhill,
Julian and Peacock, Sharon J",
abstract = "OBJECTIVES: Genome sequencing will be increasingly used in the
clinical setting to tailor antimicrobial prescribing and inform
infection control outbreaks. A recent technological innovation
that could reduce the delay between pathogen sampling and data
generation is single molecule sequencing. An example of this
technology, which is undergoing evaluation through an early
access programme, is the Oxford Nanopore MinION. METHODS: We
undertook a feasibility study on six clinically significant
pathogens, comparing the MinION to the Illumina MiSeq and PacBio
RSII platforms. Genomic DNA was prepared and sequenced using the
MinION as instructed by the manufacturer, and Illumina MiSeq and
PacBio sequencing was performed using established methods.
RESULTS: An evaluation of the accuracy of the MinION based on
sequencing of an MRSA isolate showed that error rates were higher
in the MinION reads, but provided an even coverage across the
entire genome length. The MinION detected all of the expected
carbapenemases and ESBL genes in five Gram-negative isolates and
the mecA gene in an MRSA isolate. CONCLUSIONS: The MinION can
detect the presence of acquired resistance genes, but
improvements in accuracy are needed so that antimicrobial
resistance associated with mutations in chromosomal genes can be
identified.",
journal = "J. Antimicrob. Chemother.",
volume = 70,
number = 10,
pages = "2775--2778",
month = oct,
year = 2015,
keywords = "antibiotics;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Meric2015-oq,
title = "Ecological Overlap and Horizontal Gene Transfer in Staphylococcus
aureus and Staphylococcus epidermidis",
author = "M{\'e}ric, Guillaume and Miragaia, Maria and de Been, Mark and
Yahara, Koji and Pascoe, Ben and Mageiros, Leonardos and Mikhail,
Jane and Harris, Llinos G and Wilkinson, Thomas S and Rolo, Joana
and Lamble, Sarah and Bray, James E and Jolley, Keith A and
Hanage, William P and Bowden, Rory and Maiden, Martin C J and
Mack, Dietrich and de Lencastre, Herm{\'\i}nia and Feil, Edward J
and Corander, Jukka and Sheppard, Samuel K",
abstract = "The opportunistic pathogens Staphylococcus aureus and
Staphylococcus epidermidis represent major causes of severe
nosocomial infection, and are associated with high levels of
mortality and morbidity worldwide. These species are both common
commensals on the human skin and in the nasal pharynx, but are
genetically distinct, differing at 24\% average nucleotide
divergence in 1,478 core genes. To better understand the genome
dynamics of these ecologically similar staphylococcal species, we
carried out a comparative analysis of 324 S. aureus and S.
epidermidis genomes, including 83 novel S. epidermidis sequences.
A reference pan-genome approach and whole genome
multilocus-sequence typing revealed that around half of the
genome (1,478 genes) was shared between the species. Based on a
BratNextGen analysis, homologous recombination was found to have
impacted on 40\% of the core genes in S. epidermidis, but on only
24\% of the core genes in S. aureus. Homologous recombination
between the species is rare, with a maximum of 9 gene alleles
shared between any two S. epidermidis and S. aureus isolates. In
contrast, considerable interspecies admixture is noted in mobile
elements, in particular genes associated with the SaPIn1
pathogenicity island, metal detoxification, and the
methicillin-resistance island SCCmec. Our data and analysis
provide a context for considering the nature of recombinational
boundaries between S. aureus and S. epidermidis and, the
selective forces that influence realized recombination between
these species.",
journal = "Genome Biol. Evol.",
volume = 7,
number = 5,
pages = "1313--1328",
month = apr,
year = 2015,
keywords = "Staphylococcus; ecology; evolution; nosocomial infections;
recombination;Staphylococcus;plasmid;recombination;pangenome;Staph\_evolutionary\_history;Staph\_evolutionary\_history/staph
microbial interactions;bacterial comparative
genomics;Read-lab-shared;Papers\_for\_Michelle;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers"
}
@ARTICLE{Bradley2015-zy,
title = "Rapid antibiotic-resistance predictions from genome sequence data
for Staphylococcus aureus and Mycobacterium tuberculosis",
author = "Bradley, Phelim and Gordon, N Claire and Walker, Timothy M and
Dunn, Laura and Heys, Simon and Huang, Bill and Earle, Sarah and
Pankhurst, Louise J and Anson, Luke and de Cesare, Mariateresa
and Piazza, Paolo and Votintseva, Antonina A and Golubchik, Tanya
and Wilson, Daniel J and Wyllie, David H and Diel, Roland and
Niemann, Stefan and Feuerriegel, Silke and Kohl, Thomas A and
Ismail, Nazir and Omar, Shaheed V and Smith, E Grace and Buck,
David and McVean, Gil and Walker, A Sarah and Peto, Tim E A and
Crook, Derrick W and Iqbal, Zamin",
abstract = "The rise of antibiotic-resistant bacteria has led to an urgent
need for rapid detection of drug resistance in clinical samples,
and improvements in global surveillance. Here we show how de
Bruijn graph representation of bacterial diversity can be used to
identify species and resistance profiles of clinical isolates. We
implement this method for Staphylococcus aureus and Mycobacterium
tuberculosis in a software package ('Mykrobe predictor') that
takes raw sequence data as input, and generates a
clinician-friendly report within 3 minutes on a laptop. For S.
aureus, the error rates of our method are comparable to
gold-standard phenotypic methods, with sensitivity/specificity of
99.1\%/99.6\% across 12 antibiotics (using an independent
validation set, n=470). For M. tuberculosis, our method predicts
resistance with sensitivity/specificity of 82.6\%/98.5\%
(independent validation set, n=1,609); sensitivity is lower here,
probably because of limited understanding of the underlying
genetic mechanisms. We give evidence that minor alleles improve
detection of extremely drug-resistant strains, and demonstrate
feasibility of the use of emerging single-molecule nanopore
sequencing techniques for these purposes.",
journal = "Nat. Commun.",
volume = 6,
pages = "10063",
month = dec,
year = 2015,
keywords = "Staphylococcus;antibiotics;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Garvey2016-cd,
title = "Improved understanding of an outbreak of meticillin-resistant
Staphylococcus aureus in a regional burns centre via whole-genome
sequencing",
author = "Garvey, M I and Pichon, B and Bradley, C W and Moiemen, N S and
Oppenheim, B and Kearns, A M",
journal = "J. Hosp. Infect.",
month = sep,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Bunter2016-ot,
title = "Wild type agr-negative livestock-associated {MRSA} exhibits high
adhesive capacity to human and porcine cells",
author = "B{\"u}nter, Julia P and Seth-Smith, Helena M B and R{\"u}egg,
Simon and Heikinheimo, Annamari and Borel, Nicole and Johler,
Sophia",
abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) is one of the
leading causes of nosocomial infections and a major public health
concern worldwide. During the last decade, MRSA of CC398 have
emerged as important colonizers of livestock. These strains also
represent an increasing cause of human infections. A recent study
reporting a new dominant spa type among MRSA from Finish
fattening pigs (CC398/t2741) identified a strain lacking both the
global virulence regulator gene locus agr and the adhesion gene
fnbB. The aim of this study was to characterize this
agr/fnbB-negative livestock-associated MRSA strain in terms of
growth, hemolysis and adhesive capacity, and to provide data on
its genomic background. To this end, growth curves and hemolysis
patterns were generated and adhesion assays on human keratinocyte
and porcine nasal mucosa cell lines were performed. Whole genome
sequencing was used to determine the nature and extent of the
relevant deletions in the livestock strains. For comparison, an
agr-positive, fnbB-negative CC398/t2741 strain from the same pig
herd, an agr/fnbB- positive CC398/t034 strain from another pig
herd and one human MRSA strain and its isogenic $\Delta$agr
knockout mutant were used. The agr-negative strains adhered
significantly better to human and porcine host cells than the
agr-positive control strains. For the agr-positive porcine MRSA
strains, cytotoxic effects on porcine mucosal cells were
observed. The strong adhesive capacity of the naturally
agr-negative livestock-associated MRSA, in combination with
diminished cytotoxic effects, is likely favorable for inducing
persistent colonization in pigs. Independently of the host cell
type, similar adhesive capacities of the naturally agr-negative
livestock-associated MRSA and the human MRSA strain were shown.
Our results indicate that loss of agr in the livestock-associated
MRSA strain investigated in this study may have increased its
potential to be transmitted to and amongst humans.",
journal = "Res. Microbiol.",
month = oct,
year = 2016,
keywords = "Adhesion; Livestock; MRSA; Staphylococcus aureus;
agr;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Senn2016-of,
title = "The Stealthy Superbug: the Role of Asymptomatic Enteric Carriage
in Maintaining a {Long-Term} Hospital Outbreak of {ST228}
{Methicillin-Resistant} Staphylococcus aureus",
author = "Senn, Laurence and Clerc, Olivier and Zanetti, Giorgio and
Basset, Patrick and Prod'hom, Guy and Gordon, Nicola C and
Sheppard, Anna E and Crook, Derrick W and James, Richard and
Thorpe, Harry A and Feil, Edward J and Blanc, Dominique S",
abstract = "UNLABELLED: Whole-genome sequencing (WGS) of 228 isolates was
used to elucidate the origin and dynamics of a long-term outbreak
of methicillin-resistant Staphylococcus aureus (MRSA) sequence
type 228 (ST228) SCCmec I that involved 1,600 patients in a
tertiary care hospital between 2008 and 2012. Combining of the
sequence data with detailed metadata on patient admission and
movement confirmed that the outbreak was due to the transmission
of a single clonal variant of ST228, rather than repeated
introductions of this clone into the hospital. We note that this
clone is significantly more frequently recovered from groin and
rectal swabs than other clones (P < 0.0001) and is also
significantly more transmissible between roommates (P < 0.01).
Unrecognized MRSA carriers, together with movements of patients
within the hospital, also seem to have played a major role. These
atypical colonization and transmission dynamics can help explain
how the outbreak was maintained over the long term. This
``stealthy'' asymptomatic colonization of the gut, combined with
heightened transmissibility (potentially reflecting a role for
environmental reservoirs), means the dynamics of this outbreak
share some properties with enteric pathogens such as
vancomycin-resistant enterococci or Clostridium difficile.
IMPORTANCE: Using whole-genome sequencing, we showed that a large
and prolonged outbreak of methicillin-resistant Staphylococcus
aureus was due to the clonal spread of a specific strain with
genetic elements adapted to the hospital environment.
Unrecognized MRSA carriers, the movement of patients within the
hospital, and the low detection with clinical specimens were also
factors that played a role in this occurrence. The atypical
colonization of the gut means the dynamics of this outbreak may
share some properties with enteric pathogens.",
journal = "MBio",
volume = 7,
number = 1,
pages = "e02039--15",
month = jan,
year = 2016,
keywords = "
Staphylococcus;Staph\_evolutionary\_history;Staph\_evolutionary\_history/staph
microbial interactions;bacterial comparative
genomics;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Staph\_evolution\_toxins",
language = "en"
}
@ARTICLE{Ishii2015-ur,
title = "Phenotypic and genomic comparisons of highly
vancomycin-resistant Staphylococcus aureus strains developed
from multiple clinical {MRSA} strains by in vitro mutagenesis",
author = "Ishii, Kenichi and Tabuchi, Fumiaki and Matsuo, Miki and
Tatsuno, Keita and Sato, Tomoaki and Okazaki, Mitsuhiro and
Hamamoto, Hiroshi and Matsumoto, Yasuhiko and Kaito, Chikara and
Aoyagi, Tetsuji and Hiramatsu, Keiichi and Kaku, Mitsuo and
Moriya, Kyoji and Sekimizu, Kazuhisa",
abstract = "The development of vancomycin (VCM) resistance in Staphylococcus
aureus threatens global health. Studies of the VCM-resistance
mechanism and alternative therapeutic strategies are urgently
needed. We mutagenized S. aureus laboratory strains and
methicillin-resistant S. aureus (MRSA) with ethyl
methanesulfonate, and isolated mutants that exhibited high
resistance to VCM (minimum inhibitory concentration = 32
$\mu$g/ml). These VCM-resistant strains were sensitive to
linezolid and rifampicin, and partly to arbekacin and
daptomycin. Beta-lactams had synergistic effects with VCM
against these mutants. VCM-resistant strains exhibited a 2-fold
increase in the cell wall thickness. Several genes were commonly
mutated among the highly VCM-resistant mutants. These findings
suggest that MRSA has a potential to develop high VCM resistance
with cell wall thickening by the accumulation of mutations.",
journal = "Sci. Rep.",
publisher = "ncbi.nlm.nih.gov",
volume = 5,
pages = "17092",
month = nov,
year = 2015,
keywords = "confirmed\_SA-resistance-mutation;Staphylococcus;antibiotics;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Chang2016-oa,
title = "Identifying the effect of patient sharing on between-hospital
genetic differentiation of methicillin-resistant Staphylococcus
aureus",
author = "Chang, Hsiao-Han and Dordel, Janina and Donker, Tjibbe and Worby,
Colin J and Feil, Edward J and Hanage, William P and Bentley,
Stephen D and Huang, Susan S and Lipsitch, Marc",
abstract = "BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is
one of the most common healthcare-associated pathogens. To
examine the role of inter-hospital patient sharing on MRSA
transmission, a previous study collected 2,214 samples from 30
hospitals in Orange County, California and showed by spa typing
that genetic differentiation decreased significantly with
increased patient sharing. In the current study, we focused on
the 986 samples with spa type t008 from the same population.
METHODS: We used genome sequencing to determine the effect of
patient sharing on genetic differentiation between hospitals.
Genetic differentiation was measured by between-hospital genetic
diversity, F ST , and the proportion of nearly identical isolates
between hospitals. RESULTS: Surprisingly, we found very similar
genetic diversity within and between hospitals, and no
significant association between patient sharing and genetic
differentiation measured by F ST . However, in contrast to F ST ,
there was a significant association between patient sharing and
the proportion of nearly identical isolates between hospitals. We
propose that the proportion of nearly identical isolates is more
powerful at determining transmission dynamics than traditional
estimators of genetic differentiation (F ST ) when gene flow
between populations is high, since it is more responsive to
recent transmission events. Our hypothesis was supported by the
results from coalescent simulations. CONCLUSIONS: Our results
suggested that there was a high level of gene flow between
hospitals facilitated by patient sharing, and that the proportion
of nearly identical isolates is more sensitive to population
structure than F ST when gene flow is high.",
journal = "Genome Med.",
volume = 8,
number = 1,
pages = "18",
month = feb,
year = 2016,
keywords = "Staphylococcus;Staph\_evolutionary\_history;bacterial comparative
genomics;Teaching antibiotic resistance
genomics;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers"
}
@ARTICLE{Salipante2015-qz,
title = "Application of whole-genome sequencing for bacterial strain
typing in molecular epidemiology",
author = "Salipante, Stephen J and SenGupta, Dhruba J and Cummings, Lisa A
and Land, Tyler A and Hoogestraat, Daniel R and Cookson, Brad T",
abstract = "Nosocomial infections pose a significant threat to patient
health; however, the gold standard laboratory method for
determining bacterial relatedness (pulsed-field gel
electrophoresis [PFGE]) remains essentially unchanged 20 years
after its introduction. Here, we explored bacterial whole-genome
sequencing (WGS) as an alternative approach for molecular strain
typing. We compared WGS to PFGE for investigating presumptive
outbreaks involving three important pathogens:
vancomycin-resistant Enterococcus faecium (n=19),
methicillin-resistant Staphylococcus aureus (n=17), and
Acinetobacter baumannii (n=15). WGS was highly reproducible
(average$\leq$0.39 differences between technical replicates),
which enabled a functional, quantitative definition for
determining clonality. Strain relatedness data determined by PFGE
and WGS roughly correlated, but the resolution of WGS was
superior (P=5.6$\times$10(-8) to 0.016). Several discordant
results were noted between the methods. A total of 28.9\% of
isolates which were indistinguishable by PFGE were nonclonal by
WGS. For A. baumannii, a species known to undergo rapid
horizontal gene transfer, 16.2\% of isolate pairs considered
nonidentical by PFGE were clonal by WGS. Sequencing whole
bacterial genomes with single-nucleotide resolution demonstrates
that PFGE is prone to false-positive and false-negative results
and suggests the need for a new gold standard approach for
molecular epidemiological strain typing.",
journal = "J. Clin. Microbiol.",
volume = 53,
number = 4,
pages = "1072--1079",
month = apr,
year = 2015,
keywords = "experimental\_design;Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Croucher2016-vz,
title = "Horizontal {DNA} Transfer Mechanisms of Bacteria as Weapons of
Intragenomic Conflict",
author = "Croucher, Nicholas J and Mostowy, Rafal and Wymant, Christopher
and Turner, Paul and Bentley, Stephen D and Fraser, Christophe",
abstract = "Horizontal DNA transfer (HDT) is a pervasive mechanism of
diversification in many microbial species, but its primary
evolutionary role remains controversial. Much recent research has
emphasised the adaptive benefit of acquiring novel DNA, but here
we argue instead that intragenomic conflict provides a coherent
framework for understanding the evolutionary origins of HDT. To
test this hypothesis, we developed a mathematical model of a
clonally descended bacterial population undergoing HDT through
transmission of mobile genetic elements (MGEs) and genetic
transformation. Including the known bias of transformation toward
the acquisition of shorter alleles into the model suggested it
could be an effective means of counteracting the spread of MGEs.
Both constitutive and transient competence for transformation
were found to provide an effective defence against parasitic
MGEs; transient competence could also be effective at permitting
the selective spread of MGEs conferring a benefit on their host
bacterium. The coordination of transient competence with
cell-cell killing, observed in multiple species, was found to
result in synergistic blocking of MGE transmission through
releasing genomic DNA for homologous recombination while
simultaneously reducing horizontal MGE spread by lowering the
local cell density. To evaluate the feasibility of the functions
suggested by the modelling analysis, we analysed genomic data
from longitudinal sampling of individuals carrying Streptococcus
pneumoniae. This revealed the frequent within-host coexistence of
clonally descended cells that differed in their MGE infection
status, a necessary condition for the proposed mechanism to
operate. Additionally, we found multiple examples of MGEs
inhibiting transformation through integrative disruption of genes
encoding the competence machinery across many species, providing
evidence of an ongoing ``arms race.'' Reduced rates of
transformation have also been observed in cells infected by MGEs
that reduce the concentration of extracellular DNA through
secretion of DNases. Simulations predicted that either mechanism
of limiting transformation would benefit individual MGEs, but
also that this tactic's effectiveness was limited by competition
with other MGEs coinfecting the same cell. A further observed
behaviour we hypothesised to reduce elimination by transformation
was MGE activation when cells become competent. Our model
predicted that this response was effective at counteracting
transformation independently of competing MGEs. Therefore, this
framework is able to explain both common properties of MGEs, and
the seemingly paradoxical bacterial behaviours of transformation
and cell-cell killing within clonally related populations, as the
consequences of intragenomic conflict between self-replicating
chromosomes and parasitic MGEs. The antagonistic nature of the
different mechanisms of HDT over short timescales means their
contribution to bacterial evolution is likely to be substantially
greater than previously appreciated.",
journal = "PLoS Biol.",
volume = 14,
number = 3,
pages = "e1002394",
month = mar,
year = 2016,
keywords = "systems\_biology;evolution;recombination;simulated-evolution;theory;Staph\_evolutionary\_history/Teaching\_Prokaryotic\_evolution;Staph\_evolutionary\_history;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Wang2014-uw,
title = "Comparative genomics of methicillin-resistant Staphylococcus
aureus {ST239}: distinct geographical variants in Beijing and
Hong Kong",
author = "Wang, Zheng and Zhou, Haokui and Wang, Hui and Chen, Hongbin and
Leung, K K and Tsui, Stephen and Ip, Margaret",
abstract = "BACKGROUND: The ST239 lineage is a globally disseminated,
multiply drug-resistant hospital-associated methicillin-resistant
Staphylococcus aureus (HA-MRSA). We performed whole-genome
sequencing of representative HA-MRSA isolates of the ST239
lineage from bacteremic patients in hospitals in Hong Kong (HK)
and Beijing (BJ) and compared them with three published complete
genomes of ST239, namely T0131, TW20 and JKD6008. Orthologous
gene group (OGG) analyses of the Hong Kong and Beijing cluster
strains were also undertaken. RESULTS: Homology analysis, based
on highest-percentage nucleotide identity, indicated that HK
isolates were closely related to TW20, whereas BJ isolates were
more closely related to T0131 from Tianjin. Phylogenetic
analysis, incorporating a total of 30 isolates from different
continents, revealed that strains from HK clustered with TW20
into the 'Asian clade', whereas BJ isolates and T0131 clustered
closely with strains of the 'Turkish clade' from Eastern Europe.
HK isolates contained the typical $\varphi$SP$\beta$-like
prophage with the SasX gene similar to TW20. In contrast, BJ
isolates contained a unique 15 kb PT1028-like prophage but lacked
$\varphi$SP$\beta$-like and $\varphi$SA1 prophages. Besides
distinct mobile genetic elements (MGE) in the two clusters, OGG
analyses and whole-genome alignment of these clusters highlighted
differences in genes located in the core genome, including the
identification of single nucleotide deletions in several genes,
resulting in frameshift mutations and the subsequent predicted
truncation of encoded proteins involved in metabolism and
antimicrobial resistance. CONCLUSIONS: Comparative genomics,
based on de novo assembly and deep sequencing of HK and BJ
strains, revealed different origins of the ST239 lineage in
northern and southern China and identified differences between
the two clades at single nucleotide polymorphism (SNP), core gene
and MGE levels. The results suggest that ST239 strains isolated
in Hong Kong since the 1990s belong to the Asian clade, present
mainly in southern Asia, whereas those that emerged in northern
China were of a distinct origin, reflecting the complexity of
dissemination and the dynamic evolution of this ST239 lineage.",
journal = "BMC Genomics",
volume = 15,
pages = "529",
month = jun,
year = 2014,
keywords = "Staphylococcus;bacterial comparative
genomics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Mader2016-da,
title = "Staphylococcus aureus Transcriptome Architecture: From Laboratory
to {Infection-Mimicking} Conditions",
author = "M{\"a}der, Ulrike and Nicolas, Pierre and Depke, Maren and
Pan{\'e}-Farr{\'e}, Jan and Debarbouille, Michel and van der
Kooi-Pol, Magdalena M and Gu{\'e}rin, Cyprien and D{\'e}rozier,
Sandra and Hiron, Aurelia and Jarmer, Hanne and Leduc,
Aur{\'e}lie and Michalik, Stephan and Reilman, Ewoud and
Schaffer, Marc and Schmidt, Frank and Bessi{\`e}res, Philippe and
Noirot, Philippe and Hecker, Michael and Msadek, Tarek and
V{\"o}lker, Uwe and van Dijl, Jan Maarten",
abstract = "Staphylococcus aureus is a major pathogen that colonizes about
20\% of the human population. Intriguingly, this Gram-positive
bacterium can survive and thrive under a wide range of different
conditions, both inside and outside the human body. Here, we
investigated the transcriptional adaptation of S. aureus HG001, a
derivative of strain NCTC 8325, across experimental conditions
ranging from optimal growth in vitro to intracellular growth in
host cells. These data establish an extensive repertoire of
transcription units and non-coding RNAs, a classification of 1412
promoters according to their dependence on the RNA polymerase
sigma factors SigA or SigB, and allow identification of new
potential targets for several known transcription factors. In
particular, this study revealed a relatively low abundance of
antisense RNAs in S. aureus, where they overlap only 6\% of the
coding genes, and only 19 antisense RNAs not co-transcribed with
other genes were found. Promoter analysis and comparison with
Bacillus subtilis links the small number of antisense RNAs to a
less profound impact of alternative sigma factors in S. aureus.
Furthermore, we revealed that Rho-dependent transcription
termination suppresses pervasive antisense transcription,
presumably originating from abundant spurious transcription
initiation in this A+T-rich genome, which would otherwise affect
expression of the overlapped genes. In summary, our study
provides genome-wide information on transcriptional regulation
and non-coding RNAs in S. aureus as well as new insights into the
biological function of Rho and the implications of spurious
transcription in bacteria.",
journal = "PLoS Genet.",
volume = 12,
number = 4,
pages = "e1005962",
month = apr,
year = 2016,
keywords = "Staphylococcus;rna-seq;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers;microRNA\_in\_bacteria"
}
@ARTICLE{Carroll2013-gh,
title = "Draft Genome Sequence of Strain {CBD-635}, a
{Methicillin-Resistant} Staphylococcus aureus {USA100} Isolate",
author = "Carroll, Ronan K and Burda, Whittney N and Roberts, Jill C and
Peak, Kealy K and Cannons, Andrew C and Shaw, Lindsey N",
abstract = "We present the draft genome sequence of methicillin-resistant
Staphylococcus aureus strain CBD-635, from the USA100 lineage.
This is a sepsis isolate obtained from Tampa General Hospital.
This strain is spa type t003 and multilocus sequence typing
(MLST) type ST5, and it has been used by our group in the study
of novel antimicrobial chemotherapeutics.",
journal = "Genome Announc.",
volume = 1,
number = 4,
month = jul,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Wendt2014-oh,
title = "Transmission of methicillin-resistant Staphylococcus aureus
infection through solid organ transplantation: confirmation via
whole genome sequencing",
author = "Wendt, J M and Kaul, D and Limbago, B M and Ramesh, M and Cohle,
S and Denison, A M and Driebe, E M and Rasheed, J K and Zaki, S R
and Blau, D M and Paddock, C D and McDougal, L K and Engelthaler,
D M and Keim, P S and Roe, C C and Akselrod, H and Kuehnert, M J
and Basavaraju, S V",
abstract = "We describe two cases of donor-derived methicillin-resistant
Staphylococcus aureus (MRSA) bacteremia that developed after
transplantation of organs from a common donor who died from acute
MRSA endocarditis. Both recipients developed recurrent MRSA
infection despite appropriate antibiotic therapy, and required
prolonged hospitalization and hospital readmission. Comparison of
S. aureus whole genome sequence of DNA extracted from fixed donor
tissue and recipients' isolates confirmed donor-derived
transmission. Current guidelines emphasize the risk posed by
donors with bacteremia from multidrug-resistant organisms. This
investigation suggests that, particularly in the setting of donor
endocarditis, even a standard course of prophylactic antibiotics
may not be sufficient to prevent donor-derived infection.",
journal = "Am. J. Transplant",
volume = 14,
number = 11,
pages = "2633--2639",
month = nov,
year = 2014,
keywords = "Staphylococcus;Staph\_evolutionary\_history;bacterial comparative
genomics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Tong2015-xf,
title = "Genome sequencing defines phylogeny and spread of
methicillin-resistant Staphylococcus aureus in a high
transmission setting",
author = "Tong, Steven Y C and Holden, Matthew T G and Nickerson, Emma K
and Cooper, Ben S and K{\"o}ser, Claudio U and Cori, Anne and
Jombart, Thibaut and Cauchemez, Simon and Fraser, Christophe and
Wuthiekanun, Vanaporn and Thaipadungpanit, Janjira and Hongsuwan,
Maliwan and Day, Nicholas P and Limmathurotsakul, Direk and
Parkhill, Julian and Peacock, Sharon J",
abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) is a major
cause of nosocomial infection. Whole-genome sequencing of MRSA
has been used to define phylogeny and transmission in
well-resourced healthcare settings, yet the greatest burden of
nosocomial infection occurs in resource-restricted settings where
barriers to transmission are lower. Here, we study the flux and
genetic diversity of MRSA on ward and individual patient levels
in a hospital where transmission was common. We repeatedly
screened all patients on two intensive care units for MRSA
carriage over a 3-mo period. All MRSA belonged to multilocus
sequence type 239 (ST 239). We defined the population structure
and charted the spread of MRSA by sequencing 79 isolates from 46
patients and five members of staff, including the first
MRSA-positive screen isolates and up to two repeat isolates where
available. Phylogenetic analysis identified a flux of distinct ST
239 clades over time in each intensive care unit. In total, five
main clades were identified, which varied in the carriage of
plasmids encoding antiseptic and antimicrobial resistance
determinants. Sequence data confirmed intra- and interwards
transmission events and identified individual patients who were
colonized by more than one clade. One patient on each unit was
the source of numerous transmission events, and deep sampling of
one of these cases demonstrated colonization with a ``cloud'' of
related MRSA variants. The application of whole-genome sequencing
and analysis provides novel insights into the transmission of
MRSA in under-resourced healthcare settings and has relevance to
wider global health.",
journal = "Genome Res.",
volume = 25,
number = 1,
pages = "111--118",
month = jan,
year = 2015,
keywords = "Staphylococcus;bacterial comparative
genomics;Staph\_evolutionary\_history;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Hernandez2013-xb,
title = "{Whole-Genome} Sequences of Staphylococcus aureus {ST398}
Strains of Animal Origin",
author = "Hernandez, David and van der Mee-Marquet, Nathalie and
Kluytmans, Jan and Donnio, Pierre-Yves and Quentin, Roland and
Corvaglia, Anna-Rita and Fran{\c c}ois, Patrice",
abstract = "Staphylococcus aureus sequence type 398 (ST398) was originally
associated with animal infections. We announce the complete
genome sequences of two ST398 methicillin-susceptible S. aureus
strains from the livestock environment. These genome sequences
assist in the characterization of interesting ST398 features
relying on host tropism and epidemiological settings.",
journal = "Genome Announc.",
publisher = "Am Soc Microbiol",
volume = 1,
number = 5,
month = sep,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
}
@ARTICLE{Barrado2013-dt,
title = "Draft Genome Sequence of Strain {SA\_ST125\_MupR} of
{Methicillin-Resistant} Staphylococcus aureus {ST125}, a Major
Clone in Spain",
author = "Barrado, Laura and Viedma, Esther and Vindel, Ana and Otero,
Joaqu{\'\i}n R and Chaves, Fernando",
abstract = "Here, we report the draft genome sequence of a
methicillin-resistant Staphylococcus aureus (MRSA) strain with
high-level mupirocin resistance (SA\_ST125\_MupR), isolated from
a patient with recurrent bacteremia. This strain belonged to
sequence type ST125, which was responsible for more than 50\% of
the health care-associated infections caused by MRSA in Spain.",
journal = "Genome Announc.",
publisher = "Am Soc Microbiol",
volume = 1,
number = 4,
month = aug,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Stegger2013-lf,
title = "Genome analysis of Staphylococcus aureus {ST291}, a double locus
variant of {ST398}, reveals a distinct genetic lineage",
author = "Stegger, Marc and Aziz, Maliha and Chroboczek, Tomasz and Price,
Lance B and Ronco, Troels and Kiil, Kristoffer and Skov, Robert
L and Laurent, Frederic and Andersen, Paal S",
abstract = "Staphylococcus aureus ST291 has been reported as a homologue
recombinant double locus variant of the livestock associated S.
aureus ST398. However, whole genome sequencing show that ST291
is a unique genetic lineage with highly variable content within
its accessory genome compared to both human and livestock
associated genome sequenced CC398s.",
journal = "PLoS One",
publisher = "dx.plos.org",
volume = 8,
number = 5,
pages = "e63008",
month = may,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
}
@ARTICLE{Wang2012-hj,
title = "Whole-genome sequence of Staphylococcus aureus strain
{LCT-SA112}",
author = "Wang, Junfeng and Liu, Yanhong and Wan, Daiwei and Fang,
Xiangqun and Li, Tianzhi and Guo, Yinghua and Chang, De and Su,
Longxiang and Wang, Yajuan and Zhao, Jiao and Liu, Changting",
abstract = "Staphylococcus aureus is a facultative anaerobic Gram-positive
coccal bacterium. S. aureus is the most common species of
Staphylococcus to cause staphylococcal infections, which are
very common in clinical medicine. Here we report the genome
sequence of S. aureus strain LCT-SA112, which was isolated from
S. aureus subsp. aureus CGMCC 1.230.",
journal = "J. Bacteriol.",
publisher = "Am Soc Microbiol",
volume = 194,
number = 15,
pages = "4124",
month = aug,
year = 2012,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Golding2012-pq,
title = "whole-genome sequence of livestock-associated st398
methicillin-resistant staphylococcus aureus Isolated from Humans
in Canada",
author = "Golding, George R and Bryden, Louis and Levett, Paul N and
McDonald, Ryan R and Wong, Alice and Graham, Morag R and Tyler,
Shaun and Van Domselaar, Gary and Mabon, Philip and Kent,
Heather and Butaye, Patrick and Smith, Tara C and Kadlec,
Kristina and Schwarz, Stefan and Weese, Scott J and Mulvey,
Michael R",
abstract = "Despite reports of high colonization rates of ST398
livestock-associated methicillin-resistant Staphylococcus aureus
(LA-MRSA) among pigs and pig farmers, the incidence of LA-MRSA
infection in the general population in Canada appears to be rare
in comparison to that in some European countries. In this study,
the complete genome sequence of a Canadian representative
LA-MRSA isolate (08BA02176) from a human postoperative surgical
site infection was acquired and compared to the sequenced genome
of an LA-MRSA isolate (S0385) from Europe to identify genetic
traits that may explain differences in the success of these
particular strains in some locales.",
journal = "J. Bacteriol.",
publisher = "Am Soc Microbiol",
volume = 194,
number = 23,
pages = "6627--6628",
month = dec,
year = 2012,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
}
% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Prabhakara2012-aq,
title = "Draft genome sequence of Staphylococcus aureus 118 ({ST772)}, a
major disease clone from India",
author = "Prabhakara, Sushma and Khedkar, Supriya and Loganathan, Ramya
Malarini and Chandana, S and Gowda, Malali and Arakere, Gayathri
and Seshasayee, Aswin Sai Narain",
abstract = "We report the draft genome sequence of an ST772 Staphylococcus
aureus disease isolate carrying staphylococcal cassette
chromosome mec (SCCmec) type V from a pyomyositis patient. Our
de novo short read assembly is ∼2.8 Mb and encodes a unique
Panton-Valentine leukocidin (PVL) phage with structural genes
similar to those of ϕ7247PVL and novel lysogenic genes at the N
termini.",
journal = "J. Bacteriol.",
publisher = "Am Soc Microbiol",
volume = 194,
number = 14,
pages = "3727--3728",
month = jul,
year = 2012,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Peleg2012-gx,
title = "Whole genome characterization of the mechanisms of daptomycin
resistance in clinical and laboratory derived isolates of
Staphylococcus aureus",
author = "Peleg, Anton Y and Miyakis, Spiros and Ward, Doyle V and Earl,
Ashlee M and Rubio, Aileen and Cameron, David R and Pillai,
Satish and Moellering, Jr, Robert C and Eliopoulos, George M",
abstract = "BACKGROUND: Daptomycin remains one of our last-line
anti-staphylococcal agents. This study aims to characterize the
genetic evolution to daptomycin resistance in S. aureus.
METHODS: Whole genome sequencing was performed on a unique
collection of isogenic, clinical (21 strains) and laboratory (12
strains) derived strains that had been exposed to daptomycin and
developed daptomycin-nonsusceptibility. Electron microscopy (EM)
and lipid membrane studies were performed on selected isolates.
RESULTS: On average, six coding region mutations were observed
across the genome in the clinical daptomycin exposed strains,
whereas only two mutations on average were seen in the
laboratory exposed pairs. All daptomycin-nonsusceptible strains
had a mutation in a phospholipid biosynthesis gene. This
included mutations in the previously described mprF gene, but
also in other phospholipid biosynthesis genes, including
cardiolipin synthase (cls2) and
CDP-diacylglycerol-glycerol-3-phosphate
3-phosphatidyltransferase (pgsA). EM and lipid membrane
composition analyses on two clinical pairs showed that the
daptomycin-nonsusceptible strains had a thicker cell wall and an
increase in membrane lysyl-phosphatidylglycerol. CONCLUSION:
Point mutations in genes coding for membrane phospholipids are
associated with the development of reduced susceptibility to
daptomycin in S. aureus. Mutations in cls2 and pgsA appear to be
new genetic mechanisms affecting daptomycin susceptibility in S.
aureus.",
journal = "PLoS One",
publisher = "dx.plos.org",
volume = 7,
number = 1,
pages = "e28316",
month = jan,
year = 2012,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Gasc2016-sq,
title = "Genome Sequence of Staphylococcus aureus Strain {HUK16}, Isolated
from {Hexachlorocyclohexane-Contaminated} Soil",
author = "Gasc, Cyrielle and Richard, Jean-Yves and Peyret, Pierre",
abstract = "Staphylococcus aureusstrain HUK16 has been isolated from
hexachlorocyclohexane (HCH)-long-term contaminated soil. The
genome of strain HUK16 was sequenced to understand the genetic
basis of its adaptation to HCH and to find the potential
metabolic pathways allowing it to degrade the pesticide. Here, we
report the annotated draft genome sequence (~2.7 Mbp) of this
strain.",
journal = "Genome Announc.",
volume = 4,
number = 2,
month = apr,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Hishinuma2016-wu,
title = "Complete Genome Sequence of {Vancomycin-Intermediate}
Staphylococcus aureus Strain {MI} ({HIP5827})",
author = "Hishinuma, Tomomi and Katayama, Yuki and Matsuo, Miki and Sasaki,
Takashi and Hiramatsu, Keiichi",
abstract = "We report the complete genome sequence of vancomycin-intermediate
Staphylococcus aureus (VISA) strain MI (HIP5827).",
journal = "Genome Announc.",
volume = 4,
number = 2,
month = mar,
year = 2016,
keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Marques2016-wq,
title = "Genome Sequence of a Clinical Staphylococcus aureus Strain from a
Prosthetic Joint Infection",
author = "Marqu{\`e}s, Claire and Franceschi, Christine and Collin,
Val{\'e}rie and Laurent, Fr{\'e}d{\'e}ric and Chatellier, Sonia
and Forestier, Christiane",
abstract = "Here, we report the genome sequence ofStaphylococcus
aureusLYO-S2, an isolate with sequence type (ST) 45 that was
isolated in 2001 from a prosthetic joint infection.",
journal = "Genome Announc.",
volume = 4,
number = 2,
month = apr,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Silva2016-il,
title = "Erratum for Silva et al., Draft Genome Sequences of
Staphylococcus aureus Strains Isolated from Subclinical Bovine
Mastitis in Brazil",
author = "Silva, Danielle Mendes and da Silva, M{\^o}nica Pacheco and
Vidigal, Pedro M Pereira and Barcelos, Rafael Mazioli and Klein,
Raphael Contelli and Aguilar, Ananda Pereira and Fabres-Klein,
Mary Hellen and Oliveira, Guilherme and Ribon, Andr{\'e}a
Oliveira Barros",
journal = "Genome Announc.",
volume = 4,
number = 2,
month = apr,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Abaev2016-sf,
title = "Draft Genome Sequences of Exfoliative Toxin {A-Producing}
Staphylococcus aureus Strains {B-7772} and {B-7777}
({CC8/ST2993}) and {B-7774} ({CC15/ST2126)}, Isolated in a
Maternity Hospital in the Central Federal District of Russia",
author = "Abaev, Igor and Skryabin, Yury and Kislichkina, Angelina and
Bogun, Alexandr and Korobova, Olga and Mayskaya, Nadezhda and
Shemyakin, Igor and Dyatlov, Ivan",
abstract = "Staphylococcus aureus clonal complex 8 (CC8) has not been
associated with staphylococcal scalded-skin syndrome (SSSS) in
newborns and exfoliative toxin genes. Here, we report the draft
genome sequences of exfoliative toxin A-producing B-7772, B-7777
(both CC8), and B-7774 (CC15) strains associated with SSSS in
newborns.",
journal = "Genome Announc.",
volume = 4,
number = 2,
month = mar,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Nielsen2016-bg,
title = "Fatal Septicemia Linked to Transmission of {MRSA} Clonal Complex
398 in Hospital and Nursing Home, Denmark",
author = "Nielsen, Rikke Thoft and Kemp, Michael and Holm, Anette and Skov,
Marianne Nielsine and Detlefsen, Mette and Hasman, Henrik and
Aarestrup, Frank M{\o}ller and Kaas, Rolf Sommer and Nielsen,
Jesper Boye and Westh, Henrik and Kolmos, Hans J{\o}rn",
abstract = "We describe 2 fatal cases of methicillin-resistant Staphylococcus
aureus (MRSA) clonal complex 398 septicemia in persons who had no
contact with livestock. Whole-genome sequencing of the isolated
MRSA strains strongly suggest that both were of animal origin and
that the patients had been infected through 2 independent
person-to-person transmission chains.",
journal = "Emerg. Infect. Dis.",
volume = 22,
number = 5,
pages = "900--902",
month = may,
year = 2016,
keywords = "antimicrobial resistance; bacteremia; bacteria; bacterial
infections; disease transmission; infectious; livestock;
methicillin-resistant Staphylococcus aureus; molecular
epidemiology; spa typing;
staphylococci;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Stine2016-na,
title = "Transmission Clusters of {Methicillin-Resistant} Staphylococcus
Aureus in {Long-Term} Care Facilities Based on {Whole-Genome}
Sequencing",
author = "Stine, O Colin and Burrowes, Shana and David, Sophia and Johnson,
J Kristie and Roghmann, Mary-Claire",
abstract = "OBJECTIVE To define how often methicillin-resistant
Staphylococcus aureus (MRSA) is spread from resident to resident
in long-term care facilities using whole-genome sequencing DESIGN
Prospective cohort study SETTING A long-term care facility
PARTICIPANTS Elderly residents in a long-term care facility
METHODS Cultures for MRSA were obtained weekly from multiple body
sites from residents with known MRSA colonization over 12-week
study periods. Simultaneously, cultures to detect MRSA
acquisition were obtained weekly from 2 body sites in residents
without known MRSA colonization. During the first 12-week cycle
on a single unit, we sequenced 8 MRSA isolates per swab for 2
body sites from each of 6 residents. During the second 12-week
cycle, we sequenced 30 MRSA isolates from 13 residents with known
MRSA colonization and 3 residents who had acquired MRSA
colonization. RESULTS MRSA isolates from the same swab showed
little genetic variation between isolates with the exception of
isolates from wounds. The genetic variation of isolates between
body sites on an individual was greater than that within a single
body site with the exception of 1 sample, which had 2 unrelated
strains among the 8 isolates. In the second cycle, 10 of 16
residents colonized with MRSA (63\%) shared 1 of 3 closely
related strains. Of the 3 residents with newly acquired MRSA, 2
residents harbored isolates that were members of these clusters.
CONCLUSIONS Point prevalence surveys with whole-genome sequencing
of MRSA isolates may detect resident-to-resident transmission
more accurately than routine surveillance cultures for MRSA in
long-term care facilities. Infect. Control Hosp. Epidemiol.
2016;1-7.",
journal = "Infect. Control Hosp. Epidemiol.",
pages = "1--7",
month = mar,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Davis2016-zc,
title = "Complete genome of Staphylococcus aureus Tager 104 provides
evidence of its relation to modern systemic hospital-acquired
strains",
author = "Davis, 4th, Richard W and Brannen, Andrew D and Hossain, Mohammad
J and Monsma, Scott and Bock, Paul E and Nahrendorf, Matthias and
Mead, David and Lodes, Michael and Liles, Mark R and Panizzi,
Peter",
abstract = "BACKGROUND: Staphylococcus aureus (S. aureus) infections range in
severity due to expression of certain virulence factors encoded
on mobile genetic elements (MGE). As such, characterization of
these MGE, as well as single nucleotide polymorphisms, is of high
clinical and microbiological importance. To understand the
evolution of these dangerous pathogens, it is paramount to define
reference strains that may predate MGE acquisition. One such
candidate is S. aureus Tager 104, a previously uncharacterized
strain isolated from a patient with impetigo in 1947. RESULTS: We
show here that S. aureus Tager 104 can survive in the bloodstream
and infect na{\"\i}ve organs. We also demonstrate a procedure to
construct and validate the assembly of S. aureus genomes, using
Tager 104 as a proof-of-concept. In so doing, we bridged
confounding gap regions that limited our initial attempts to
close this 2.82 Mb genome, through integration of data from
Illumina Nextera paired-end, PacBio RS, and Lucigen NxSeq
mate-pair libraries. Furthermore, we provide independent
confirmation of our segmental arrangement of the Tager 104 genome
by the sole use of Lucigen NxSeq libraries filled by paired-end
MiSeq reads and alignment with SPAdes software. Genomic analysis
of Tager 104 revealed limited MGE, and a $\nu$Sa$\beta$ island
configuration that is reminiscent of other hospital acquired S.
aureus genomes. CONCLUSIONS: Tager 104 represents an
early-branching ancestor of certain hospital-acquired strains.
Combined with its earlier isolation date and limited content of
MGE, Tager 104 can serve as a viable reference for future
comparative genome studies.",
journal = "BMC Genomics",
volume = 17,
number = 1,
pages = "179",
month = mar,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Silva2016-rh,
title = "Draft Genome Sequences of Staphylococcus aureus Strains Isolated
from Subclinical Bovine Mastitis in Brazil",
author = "Silva, Danielle Mendes and da Silva, M{\^o}nica Pacheco and
Vidigal, Pedro M Pereira and Barcelos, Rafael Mazioli and Klein,
Raphael Contelli and Aguilar, Ananda Pereira and Fabres-Klein,
Mary Hellen and Oliveira, Guilherme and Ribon, Andr{\'e}a
Oliveira Barros",
abstract = "Here, we present the draft genome sequences of four
Staphylococcus aureus strains isolated from mastitic milk
collected from animals with subclinical manifestations. Three of
them were typed as sequence type 126 (ST126), a genotype with no
genome sequence available. ST126 is found in several herds of
southern Brazil and is described as a bovine pathogen strongly
associated with milk around the world.",
journal = "Genome Announc.",
volume = 4,
number = 1,
month = feb,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Greninger2016-yp,
title = "{Whole-Genome} Sequencing of {Methicillin-Resistant}
Staphylococcus aureus Resistant to {Fifth-Generation}
Cephalosporins Reveals Potential {Non-mecA} Mechanisms of
Resistance",
author = "Greninger, Alexander L and Chatterjee, Som S and Chan, Liana C
and Hamilton, Stephanie M and Chambers, Henry F and Chiu, Charles
Y",
abstract = "Fifth-generation cephalosporins, ceftobiprole and ceftaroline,
are promising drugs for treatment of bacterial infections from
methicillin-resistant Staphylococcus aureus (MRSA). These
antibiotics are able to bind native PBP2a, the penicillin-binding
protein encoded by the mecA resistance determinant that mediates
broad class resistance to nearly all other beta-lactam
antibiotics, at clinically achievable concentrations. Mechanisms
of resistance to ceftaroline based on mecA mutations have been
previously described. Here we compare the genomes of 11 total
parent-daughter strains of Staphylococcus aureus for which
specific selection by serial passaging with ceftaroline or
ceftobiprole was used to identify novel non-mecA mechanisms of
resistance. All 5 ceftaroline-resistant strains, derived from 5
different parental strains, contained mutations directly upstream
of the pbp4 gene (coding for the PBP4 protein), including four
with the same thymidine insertion located 377 nucleotides
upstream of the promoter site. In 4 of 5 independent
ceftaroline-driven selections, we also isolated mutations to the
same residue (Asn138) in PBP4. In addition, mutations in
additional candidate genes such as ClpX endopeptidase, PP2C
protein phosphatase and transcription terminator Rho, previously
undescribed in the context of resistance to ceftaroline or
ceftobiprole, were detected in multiple selections. These genomic
findings suggest that non-mecA mechanisms, while yet to be
encountered in the clinical setting, may also be important in
mediating resistance to 5th-generation cephalosporins.",
journal = "PLoS One",
volume = 11,
number = 2,
pages = "e0149541",
month = feb,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Khan2016-ez,
title = "Draft Genome Sequences of Two {Methicillin-Resistant} Clinical
Staphylococcus aureus Isolates",
author = "Khan, Saeed and Sung, Kidon and Iram, Saira and Nawaz, Mohamed
and Xu, Joshua and Marasa, Bernard",
abstract = "Here, we report the draft genome sequences of two
methicillin-resistant Staphylococcus aureus (MRSA) clinical
isolates, hospital-associated perirectal isolate 32S (ST 239)
from a colitis tracheostomy patient and community-associated MRSA
isolate 42S (ST 772) from a hepatic-splenomegaly patient in
Rawalpindi, Pakistan.",
journal = "Genome Announc.",
volume = 4,
number = 1,
month = feb,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Holmes2016-yn,
title = "Genomic Analysis of Companion Rabbit Staphylococcus aureus",
author = "Holmes, Mark A and Harrison, Ewan M and Fisher, Elizabeth A and
Graham, Elizabeth M and Parkhill, Julian and Foster, Geoffrey and
Paterson, Gavin K",
abstract = "In addition to being an important human pathogen, Staphylococcus
aureus is able to cause a variety of infections in numerous other
host species. While the S. aureus strains causing infection in
several of these hosts have been well characterised, this is not
the case for companion rabbits (Oryctolagus cuniculus), where
little data are available on S. aureus strains from this host. To
address this deficiency we have performed antimicrobial
susceptibility testing and genome sequencing on a collection of
S. aureus isolates from companion rabbits. The findings show a
diverse S. aureus population is able to cause infection in this
host, and while antimicrobial resistance was uncommon, the
isolates possess a range of known and putative virulence factors
consistent with a diverse clinical presentation in companion
rabbits including severe abscesses. We additionally show that
companion rabbit isolates carry polymorphisms within dltB as
described as underlying host-adaption of S. aureus to farmed
rabbits. The availability of S. aureus genome sequences from
companion rabbits provides an important aid to understanding the
pathogenesis of disease in this host and in the clinical
management and surveillance of these infections.",
journal = "PLoS One",
volume = 11,
number = 3,
pages = "e0151458",
month = mar,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
}
@ARTICLE{Kong2016-eb,
title = "{Whole-Genome} Sequencing for the Investigation of a Hospital
Outbreak of {MRSA} in China",
author = "Kong, Zhenzhen and Zhao, Peipei and Liu, Haibing and Yu, Xiang
and Qin, Yanyan and Su, Zhaoliang and Wang, Shengjun and Xu,
Huaxi and Chen, Jianguo",
abstract = "Staphylococcus aureus is a globally disseminated drug-resistant
bacterial species. It remains a leading cause of
hospital-acquired infection, primarily among immunocompromised
patients. In 2012, the Affiliated People's Hospital of Jiangsu
University experienced a putative outbreak of
methicillin-resistant S. aureus (MRSA) that affected 12 patients
in the Neurosurgery Department. In this study, whole-genome
sequencing (WGS) was used to gain insight into the epidemiology
of the outbreak caused by MRSA, and traditional bacterial
genotyping approaches were also applied to provide supportive
evidence for WGS. We sequenced the DNA from 6 isolates associated
with the outbreak. Phylogenetic analysis was constructed by
comparing single-nucleotide polymorphisms (SNPs) in the core
genome of 6 isolates in the present study and another 3
referenced isolates from GenBank. Of the 6 MRSA sequences in the
current study, 5 belonged to the same group, clustering with
T0131, while the other one clustered closely with TW20. All of
the isolates were identified as ST239-SCCmecIII clones.
Whole-genome analysis revealed that four of the outbreak isolates
were more tightly clustered into a group and SA13002 together
with SA13009 were distinct from the outbreak strains, which were
considered non-outbreak strains. Based on the sequencing results,
the antibiotic-resistance gene status (present or absent) was
almost perfectly concordant with the results of phenotypic
susceptibility testing. Various toxin genes were also analyzed
successfully. Our analysis demonstrates that using traditional
molecular methods and WGS can facilitate the identification of
outbreaks and help to control nosocomial transmission.",
journal = "PLoS One",
volume = 11,
number = 3,
pages = "e0149844",
month = mar,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Sidjabat2015-nx,
title = "Draft Genome Sequences of Burkholderia pseudomallei and
Staphylococcus aureus, Isolated from a Patient with Chronic
Rhinosinusitis",
author = "Sidjabat, Hanna E and Cottrell, Kyra and Cervin, Anders",
abstract = "Here, we report the draft genome sequences of Burkholderia
pseudomallei and Staphylococcus aureus causing chronic
rhinosinusitis. Whole-genome sequencing determined the B.
pseudomallei as sequence type (ST) 1381 and the S. aureus as ST8.
B. pseudomallei possessed the blaOXA-59 gene. This study
illustrates the potential emergence of B. pseudomallei in cases
of chronic rhinosinusitis.",
journal = "Genome Announc.",
volume = 3,
number = 5,
month = oct,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Sharma2015-mr,
title = "Draft Genome Sequence of a Staphylococcus aureus Strain Isolated
from a Cow with Clinical Mastitis",
author = "Sharma, Paresh and Reddy, D Peddi and Kumar, P Anand and
Gadicherla, Ramya and George, Neena and Bhandari, Vasundhra",
abstract = "We report here the draft genome of Staphylococcus aureus causing
clinical mastitis in a cow from India. It is a major causative
agent of mastitis and, further, livestock-associated strains are
emerging as a potential threat to public health, thereby
warranting studies to understand the genome of this deadly
pathogen.",
journal = "Genome Announc.",
volume = 3,
number = 4,
month = aug,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Soni2015-tm,
title = "Draft Genome Sequence of {Methicillin-Sensitive} Staphylococcus
aureus {ATCC} 29213",
author = "Soni, Isha and Chakrapani, Harinath and Chopra, Sidharth",
abstract = "Staphylococcus aureus subsp. aureus ATCC 29213 is one of the most
commonly used strains in drug discovery research and for quality
control. We report the completed draft genome sequence for the
strain.",
journal = "Genome Announc.",
volume = 3,
number = 5,
month = sep,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Marasa2015-ve,
title = "Draft Genome Sequence of {Methicillin-Resistant} Clinical
Staphylococcus aureus Isolate {51S} (Sequence Type 291)",
author = "Marasa, Bernard S and Khan, Saeed and Iram, Saira and Sung, Kidon
and Xu, Joshua",
abstract = "We report the draft genome sequence of a methicillin-resistant
clinical Staphylococcus aureus isolate with a novel spa type and
sequence type (ST291), isolated from a renal failure patient in
Rawalpindi, Pakistan.",
journal = "Genome Announc.",
volume = 3,
number = 5,
month = sep,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Budd2015-ry,
title = "Extensive Genomic Diversity among {Bovine-Adapted} Staphylococcus
aureus: Evidence for a Genomic Rearrangement within {CC97}",
author = "Budd, Kathleen E and McCoy, Finola and Monecke, Stefan and
Cormican, Paul and Mitchell, Jennifer and Keane, Orla M",
abstract = "Staphylococcus aureus is an important pathogen associated with
both human and veterinary disease and is a common cause of bovine
mastitis. Genomic heterogeneity exists between S. aureus strains
and has been implicated in the adaptation of specific strains to
colonise particular mammalian hosts. Knowledge of the factors
required for host specificity and virulence is important for
understanding the pathogenesis and management of S. aureus
mastitis. In this study, a panel of mastitis-associated S. aureus
isolates (n = 126) was tested for resistance to antibiotics
commonly used to treat mastitis. Over half of the isolates (52\%)
demonstrated resistance to penicillin and ampicillin but all were
susceptible to the other antibiotics tested. S. aureus isolates
were further examined for their clonal diversity by Multi-Locus
Sequence Typing (MLST). In total, 18 different sequence types
(STs) were identified and eBURST analysis demonstrated that the
majority of isolates grouped into clonal complexes CC97, CC151 or
sequence type (ST) 136. Analysis of the role of recombination
events in determining S. aureus population structure determined
that ST diversification through nucleotide substitutions were
more likely to be due to recombination compared to point
mutation, with regions of the genome possibly acting as
recombination hotspots. DNA microarray analysis revealed a large
number of differences amongst S. aureus STs in their variable
genome content, including genes associated with capsule and
biofilm formation and adhesion factors. Finally, evidence for a
genomic arrangement was observed within isolates from CC97 with
the ST71-like subgroup showing evidence of an IS431 insertion
element having replaced approximately 30 kb of DNA including the
ica operon and histidine biosynthesis genes, resulting in
histidine auxotrophy. This genomic rearrangement may be
responsible for the diversification of ST71 into an emerging
bovine adapted subgroup.",
journal = "PLoS One",
volume = 10,
number = 8,
pages = "e0134592",
month = aug,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Shiroma2015-ho,
title = "First Complete Genome Sequences of Staphylococcus aureus subsp.
aureus Rosenbach 1884 ({DSM} 20231T), Determined by {PacBio}
{Single-Molecule} {Real-Time} Technology",
author = "Shiroma, Akino and Terabayashi, Yasunobu and Nakano, Kazuma and
Shimoji, Makiko and Tamotsu, Hinako and Ashimine, Noriko and
Ohki, Shun and Shinzato, Misuzu and Teruya, Kuniko and Satou,
Kazuhito and Hirano, Takashi",
abstract = "The first complete genome sequences of Staphylococcus aureus
subsp. aureus Rosenbach 1884 strain DSM 20231(T), the type strain
of the bacterium causing staphylococcal disease, were determined
using PacBio RS II. The sequences represent the chromosome
(2,755,072 bp long; G+C content, 32.86\%) and a plasmid (27,490
bp long; G+C content, 30.69\%).",
journal = "Genome Announc.",
volume = 3,
number = 4,
month = jul,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Stephens2015-kc,
title = "Draft Genome Sequence of a {Community-Associated}
{Methicillin-Resistant} {Panton-Valentine} {Leukocidin-Positive}
Staphylococcus aureus Sequence Type 30 Isolate from a Pediatric
Patient with a Lung Infection in Brazil",
author = "Stephens, Craig and Cho, Paul Jang-Yeon and Afonso de Araujo,
Veronica and Gomes, Ivete Martins and de Azevedo Sias, Selma
Maria and Ara{\'u}jo Cardoso, Claudete A and Riley, Lee W and
Aguiar-Alves, F{\'a}bio",
abstract = "The sequence of methicillin-resistant Staphylococcus aureus
strain B6 (sequence type 30 [ST30], spa type t433, staphylococcal
chromosomal cassette mec element [SCCmec] type IVc,
Panton-Valentine leukocidin [PVL] positive), isolated from a
pediatric patient with a lung infection in Niter{\'o}i, Rio de
Janeiro, Brazil, is described here. The draft genome sequence
includes a 2.8-Mb chromosome, accompanied by a 20-kb plasmid
containing blaZ and two small cryptic plasmids.",
journal = "Genome Announc.",
volume = 3,
number = 4,
month = aug,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Nemet2015-mo,
title = "Draft Genome Sequence of a Highly Virulent Rabbit Staphylococcus
aureus Strain",
author = "N{\'e}met, Zolt{\'a}n and Albert, Ervin and Nagy, Tibor and
Olasz, Ferenc and Barta, Endre and Kiss, J{\'a}nos and D{\'a}n,
{\'A}d{\'a}m and B{\'a}nyai, Kriszti{\'a}n and Hermans, Katleen
and Biksi, Imre",
abstract = "We report the draft genome sequence of Staphylococcus aureus
Sp17, a typical highly virulent (HV) rabbit strain. As current
medicine apparently fails to effectively reduce disease and
economical losses caused by this organism, it is essential to
gain better insight on its genomic arrangement.",
journal = "Genome Announc.",
volume = 3,
number = 4,
month = jul,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Driebe2015-ia,
title = "Using Whole Genome Analysis to Examine Recombination across
Diverse Sequence Types of Staphylococcus aureus",
author = "Driebe, Elizabeth M and Sahl, Jason W and Roe, Chandler and
Bowers, Jolene R and Schupp, James M and Gillece, John D and
Kelley, Erin and Price, Lance B and Pearson, Talima R and Hepp,
Crystal M and Brzoska, Pius M and Cummings, Craig A and Furtado,
Manohar R and Andersen, Paal S and Stegger, Marc and Engelthaler,
David M and Keim, Paul S",
abstract = "Staphylococcus aureus is an important clinical pathogen worldwide
and understanding this organism's phylogeny and, in particular,
the role of recombination, is important both to understand the
overall spread of virulent lineages and to characterize
outbreaks. To further elucidate the phylogeny of S. aureus, 35
diverse strains were sequenced using whole genome sequencing. In
addition, 29 publicly available whole genome sequences were
included to create a single nucleotide polymorphism (SNP)-based
phylogenetic tree encompassing 11 distinct lineages. All strains
of a particular sequence type fell into the same clade with clear
groupings of the major clonal complexes of CC8, CC5, CC30, CC45
and CC1. Using a novel analysis method, we plotted the homoplasy
density and SNP density across the whole genome and found
evidence of recombination throughout the entire chromosome, but
when we examined individual clonal lineages we found very little
recombination. However, when we analyzed three branches of
multiple lineages, we saw intermediate and differing levels of
recombination between them. These data demonstrate that in S.
aureus, recombination occurs across major lineages that
subsequently expand in a clonal manner. Estimated mutation rates
for the CC8 and CC5 lineages were different from each other.
While the CC8 lineage rate was similar to previous studies, the
CC5 lineage was 100-fold greater. Fifty known virulence genes
were screened in all genomes in silico to determine their
distribution across major clades. Thirty-three genes were present
variably across clades, most of which were not constrained by
ancestry, indicating horizontal gene transfer or gene loss.",
journal = "PLoS One",
volume = 10,
number = 7,
pages = "e0130955",
month = jul,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Cameron2015-vs,
title = "Draft Genome Sequences of Clinical {Daptomycin-Nonsusceptible}
{Methicillin-Resistant} Staphylococcus aureus Strain {APS211} and
Its {Daptomycin-Susceptible} Progenitor {APS210}",
author = "Cameron, David R and Jiang, Jhih-Hang and Abbott, Iain J and
Spelman, Denis W and Peleg, Anton Y",
abstract = "To assess the genetic factors contributing to daptomycin
resistance in Staphylococcus aureus, the draft genome of a
clinically derived daptomycin-nonsusceptible isolate APS211 was
generated and compared to the draft sequence of its susceptible
progenitor strain APS210. Four genetic differences were
identified including a previously described mutation within the
mprF gene.",
journal = "Genome Announc.",
volume = 3,
number = 3,
month = jun,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Crovadore2015-vb,
title = "{Whole-Genome} Sequences of 15 Strains of Staphylococcus aureus
subsp. aureus Isolated from Foodstuff and Human Clinical Samples",
author = "Crovadore, Julien and Calmin, Gautier and Tonacini, Jenna and
Chablais, Romain and Baumgartner, Andreas and Schnyder, Bruno and
Hodille, Elisabeth and Lefort, Fran{\c c}ois",
abstract = "The whole-genome sequences of 15 strains of Staphylococcus aureus
(10 strains isolated from foodstuff samples in Switzerland and
five from human clinical samples) were obtained by Illumina
sequencing. Most strains fit within the known diversity for the
species, but one (SA-120) possessed a higher G+C content and a
higher number of genes than usual.",
journal = "Genome Announc.",
volume = 3,
number = 3,
month = jun,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Botka2015-wl,
title = "Complete genome analysis of two new bacteriophages isolated from
impetigo strains of Staphylococcus aureus",
author = "Botka, Tibor and R{\r u}{\v z}i{\v c}kov{\'a}, Vladislava and
Kone{\v c}n{\'a}, Hana and Pant{\r u}{\v c}ek, Roman and
Rychl{\'\i}k, Ivan and Zdr{\'a}hal, Zbyn{\v e}k and Petr{\'a}{\v
s}, Petr and Do{\v s}ka{\v r}, Ji{\v r}{\'\i}",
abstract = "Exfoliative toxin A (ETA)-coding temperate bacteriophages are
leading contributors to the toxic phenotype of impetigo strains
of Staphylococcus aureus. Two distinct eta gene-positive
bacteriophages isolated from S. aureus strains which recently
caused massive outbreaks of pemphigus neonatorum in Czech
maternity hospitals were characterized. The phages, designated
ϕB166 and ϕB236, were able to transfer the eta gene into a
prophageless S. aureus strain which afterwards converted into an
ETA producer. Complete phage genome sequences were determined,
and a comparative analysis of five designed genomic regions
revealed major variances between them. They differed in the
genome size, number of open reading frames, genome architecture,
and virion protein patterns. Their high mutual sequence
similarity was detected only in the terminal regions of the
genome. When compared with the so far described eta phage
genomes, noticeable differences were found. Thus, both phages
represent two new lineages of as yet not characterized
bacteriophages of the Siphoviridae family having impact on
pathogenicity of impetigo strains of S. aureus.",
journal = "Virus Genes",
volume = 51,
number = 1,
pages = "122--131",
month = aug,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Planet2015-jk,
title = "Parallel Epidemics of {Community-Associated}
{Methicillin-Resistant} Staphylococcus aureus {USA300} Infection
in North and South America",
author = "Planet, Paul J and Diaz, Lorena and Kolokotronis, Sergios-Orestis
and Narechania, Apurva and Reyes, Jinnethe and Xing, Galen and
Rincon, Sandra and Smith, Hannah and Panesso, Diana and Ryan,
Chanelle and Smith, Dylan P and Guzman, Manuel and Zurita,
Jeannete and Sebra, Robert and Deikus, Gintaras and Nolan, Rathel
L and Tenover, Fred C and Weinstock, George M and Robinson, D
Ashley and Arias, Cesar A",
abstract = "BACKGROUND: The community-associated methicillin-resistant
Staphylococcus aureus (CA-MRSA) epidemic in the United States is
attributed to the spread of the USA300 clone. An epidemic of
CA-MRSA closely related to USA300 has occurred in northern South
America (USA300 Latin-American variant, USA300-LV). Using
phylogenomic analysis, we aimed to understand the relationships
between these 2 epidemics. METHODS: We sequenced the genomes of
51 MRSA clinical isolates collected between 1999 and 2012 from
the United States, Colombia, Venezuela, and Ecuador. Phylogenetic
analysis was used to infer the relationships and times since the
divergence of the major clades. RESULTS: Phylogenetic analyses
revealed 2 dominant clades that segregated by geographical
region, had a putative common ancestor in 1975, and originated in
1989, in North America, and in 1985, in South America. Emergence
of these parallel epidemics coincides with the independent
acquisition of the arginine catabolic mobile element (ACME) in
North American isolates and a novel copper and mercury resistance
(COMER) mobile element in South American isolates. CONCLUSIONS:
Our results reveal the existence of 2 parallel USA300 epidemics
that shared a recent common ancestor. The simultaneous rapid
dissemination of these 2 epidemic clades suggests the presence of
shared, potentially convergent adaptations that enhance fitness
and ability to spread.",
journal = "J. Infect. Dis.",
volume = 212,
number = 12,
pages = "1874--1882",
month = dec,
year = 2015,
keywords = "MRSA; USA300; USA300-LV;
epidemics;Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers"
}
@ARTICLE{Khokhlova2015-lr,
title = "Healthcare- and {Community-Associated} {Methicillin-Resistant}
Staphylococcus aureus ({MRSA}) and Fatal Pneumonia with Pediatric
Deaths in Krasnoyarsk, Siberian Russia: Unique {MRSA's} Multiple
Virulence Factors, Genome, and Stepwise Evolution",
author = "Khokhlova, Olga E and Hung, Wei-Chun and Wan, Tsai-Wen and Iwao,
Yasuhisa and Takano, Tomomi and Higuchi, Wataru and Yachenko,
Svetlana V and Teplyakova, Olga V and Kamshilova, Vera V and
Kotlovsky, Yuri V and Nishiyama, Akihito and Reva, Ivan V and
Sidorenko, Sergey V and Peryanova, Olga V and Reva, Galina V and
Teng, Lee-Jene and Salmina, Alla B and Yamamoto, Tatsuo",
abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) is a common
multidrug-resistant (MDR) pathogen. We herein discussed MRSA and
its infections in Krasnoyarsk, Siberian Russia between 2007 and
2011. The incidence of MRSA in 3,662 subjects was 22.0\% and
2.9\% for healthcare- and community-associated MRSA (HA- and
CA-MRSA), respectively. The 15-day mortality rates for MRSA
hospital- and community-acquired pneumonia (HAP and CAP) were
6.5\% and 50\%, respectively. MRSA CAP cases included pediatric
deaths; of the MRSA pneumonia episodes available, $\geq$27.3\%
were associated with bacteremia. Most cases of HA-MRSA examined
exhibited ST239/spa3(t037)/SCCmecIII.1.1.2 (designated as
ST239Kras), while all CA-MRSA cases examined were
ST8/spa1(t008)/SCCmecIV.3.1.1(IVc) (designated as ST8Kras).
ST239Kras and ST8Kras strongly expressed cytolytic peptide
(phenol-soluble modulin $\alpha$, PSM$\alpha$; and
$\delta$-hemolysin, Hld) genes, similar to CA-MRSA. ST239Kras
pneumonia may have been attributed to a unique set of multiple
virulence factors (MVFs): toxic shock syndrome toxin-1 (TSST-1),
elevated PSM$\alpha$/Hld expression, $\alpha$-hemolysin, the
staphylococcal enterotoxin SEK/SEQ, the immune evasion factor
SCIN/SAK, and collagen adhesin. Regarding ST8Kras, SEA was
included in MVFs, some of which were common to ST239Kras. The
ST239Kras (strain OC3) genome contained: a completely unique
phage, $\varphi$Sa7-like (W), with no att repetition; S. aureus
pathogenicity island SaPI2R, the first TSST-1 gene-positive
(tst+) SaPI in the ST239 lineage; and a super copy of IS256
($\geq$22 copies/genome). ST239Kras carried the Brazilian
SCCmecIII.1.1.2 and United Kingdom-type tst. ST239Kras and
ST8Kras were MDR, with the same levofloxacin resistance
mutations; small, but transmissible chloramphenicol resistance
plasmids spread widely enough to not be ignored. These results
suggest that novel MDR and MVF+ HA- and CA-MRSA (ST239Kras and
ST8Kras) emerged in Siberian Russia (Krasnoyarsk) associated with
fatal pneumonia, and also with ST239Kras, a new (Siberian
Russian) clade of the ST239 lineage, which was created through
stepwise evolution during its potential transmission route of
Brazil-Europe-Russia/Krasnoyarsk, thereby selective advantages
from unique MVFs and the MDR.",
journal = "PLoS One",
volume = 10,
number = 6,
pages = "e0128017",
month = jun,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Aalbaek2015-be,
title = "{Whole-Genome} Sequence of Staphylococcus aureus {S54F9} Isolated
from a Chronic Disseminated Porcine Lung Abscess and Used in
Human Infection Models",
author = "Aalb{\ae}k, Bent and Jensen, Louise Kruse and Jensen, Henrik
Elvang and Olsen, John Elmerdahl and Christensen, Henrik",
abstract = "We obtained a draft genome sequence of Staphylococcus aureus
strain S54F9, which was isolated from a chronic disseminated
porcine lung abscess and used in porcine infection models. Genes
coding for a number of toxins, including enterotoxins and
superantigen, were demonstrated in this strain.",
journal = "Genome Announc.",
volume = 3,
number = 5,
month = oct,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Chang2015-gk,
title = "Isolation and Genome Characterization of the Virulent
Staphylococcus aureus Bacteriophage {SA97}",
author = "Chang, Yoonjee and Shin, Hakdong and Lee, Ju-Hoon and Park, Chul
Jong and Paik, Soon-Young and Ryu, Sangryeol",
abstract = "A novel bacteriophage that infects S. aureus, SA97, was isolated
and characterized. The phage SA97 belongs to the Siphoviridae
family, and the cell wall teichoic acid (WTA) was found to be a
host receptor of the phage SA97. Genome analysis revealed that
SA97 contains 40,592 bp of DNA encoding 54 predicted open reading
frames (ORFs), and none of these genes were related to virulence
or drug resistance. Although a few genes associated with lysogen
formation were detected in the phage SA97 genome, the phage SA97
produced neither lysogen nor transductant in S. aureus. These
results suggest that the phage SA97 may be a promising candidate
for controlling S. aureus.",
journal = "Viruses",
volume = 7,
number = 10,
pages = "5225--5242",
month = oct,
year = 2015,
keywords = "Staphylococcus aureus; bacteriophage; genome
analysis;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Richards2015-mm,
title = "Persistent Staphylococcus aureus isolates from two independent
cases of bacteremia display increased bacterial fitness and novel
immune evasion phenotypes",
author = "Richards, R L and Haigh, R D and Pascoe, B and Sheppard, S K and
Price, F and Jenkins, D and Rajakumar, K and Morrissey, J A",
abstract = "Staphylococcus aureus bacteremia cases are complicated by
bacterial persistence and treatment failure despite the confirmed
in vitro susceptibility of the infecting strain to administered
antibiotics. A high incidence of methicillin-resistant S. aureus
(MRSA) bacteremia cases are classified as persistent and are
associated with poorer patient outcomes. It is still unclear how
S. aureus evades the host immune system and resists antibiotic
treatment for the prolonged duration of a persistent infection.
In this study, the genetic changes and associated phenotypic
traits specific to S. aureus persistent bacteremia were
identified by comparing temporally dispersed isolates from
persistent infections (persistent isolates) originating from two
independent persistent S. aureus bacteremia cases with the
initial infection isolates and with three resolved S. aureus
bacteremia isolates from the same genetic background. Several
novel traits were associated specifically with both independent
sets of persistent S. aureus isolates compared to both the
initial isolates and the isolates from resolved infections
(resolved isolates). These traits included (i) increased growth
under nutrient-poor conditions; (ii) increased tolerance of iron
toxicity; (iii) higher expression of cell surface proteins
involved in immune evasion and stress responses; and (iv)
attenuated virulence in a Galleria mellonella larva infection
model that was not associated with small-colony variation or
metabolic dormancy such as had been seen previously. Whole-genome
sequence analysis identified different single nucleotide
mutations within the mprF genes of all the isolates with the
adaptive persistence traits from both independent cases. Overall,
our data indicate a novel role for MprF function during
development of S. aureus persistence by increasing bacterial
fitness and immune evasion.",
journal = "Infect. Immun.",
volume = 83,
number = 8,
pages = "3311--3324",
month = aug,
year = 2015,
keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;biometals;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers"
}
@ARTICLE{Sabat2015-jb,
title = "Whole-genome analysis of an oxacillin-susceptible {CC80}
mecA-positive Staphylococcus aureus clinical isolate: insights
into the mechanisms of cryptic methicillin resistance",
author = "Sabat, Artur J and Pournaras, Spyros and Akkerboom, Viktoria and
Tsakris, Athanassios and Grundmann, Hajo and Friedrich, Alexander
W",
abstract = "OBJECTIVES: The mec and bla systems, among other genetic factors,
are critical in regulating the expression of methicillin
resistance in Staphylococcus aureus. We examined by WGS a
naturally occurring oxacillin-susceptible mecA-positive S. aureus
isolate to identify the mechanism conferring oxacillin
susceptibility. METHODS: The mecA-positive oxacillin-susceptible
S. aureus isolate GR2 (penicillin and oxacillin MICs 0.094 and 1
mg/L, respectively), belonging to clonal complex 80, was
characterized. DNA fragment libraries were sequenced on Roche 454
and Illumina MiSeq sequencers and de novo assembly of the genome
was generated using SeqMan NGen software. Plasmid curing was
conducted by SDS treatment. Expression of mecA was quantified
without/with $\beta$-lactam pressure. RESULTS: The genome of GR2
consisted of a 2 792 802 bp chromosome and plasmids pGR2A (28 895
bp) and pGR2B (2473 bp). GR2 carried SCCmec type IV, with a
truncated/non-functional mecR1 gene and no mecI. A single copy of
the bla system, with an organization unique for S. aureus, was
found, harboured by plasmid pGR2A. Particularly, the blaZ gene
was orientated like its regulatory genes, blaI and blaR1, and a
gene encoding transposase IS66 was integrated between blaZ and
the regulatory genes deleting the 5'-end of blaR1; blaI, encoding
blaZ/mecA repressor, was intact. After plasmid loss, GR2 became
penicillin and oxacillin resistant (MICs 0.5 and 6 mg/L,
respectively). CONCLUSIONS: We can conclude that after exposure
to $\beta$-lactams, the non-functional BlaR1 does not cleave the
mecA repressor BlaI, derepression does not occur and mecA is not
efficiently expressed. Removal of the bla system after curing of
pGR2A allows constitutive expression of mecA, resulting in
oxacillin and penicillin resistance.",
journal = "J. Antimicrob. Chemother.",
volume = 70,
number = 11,
pages = "2956--2964",
month = nov,
year = 2015,
keywords = "Staphylococcus;oxacillin;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Hamed2015-om,
title = "Whole genome sequence typing and microarray profiling of nasal
and blood stream methicillin-resistant Staphylococcus aureus
isolates: Clues to phylogeny and invasiveness",
author = "Hamed, Mohamed and Nitsche-Schmitz, Daniel Patric and Ruffing,
Ulla and Steglich, Matthias and Dordel, Janina and Nguyen, Duy
and Brink, Jan-Hendrik and Chhatwal, Gursharan Singh and
Herrmann, Mathias and N{\"u}bel, Ulrich and Helms, Volkhard and
von M{\"u}ller, Lutz",
abstract = "Hospital-associated methicillin-resistant Staphylococcus aureus
(MRSA) infections are frequently caused by predominant clusters
of closely related isolates that cannot be discriminated by
conventional diagnostic typing methods. Whole genome sequencing
(WGS) and DNA microarray (MA) now allow for better discrimination
within a prevalent clonal complex (CC). This single center
exploratory study aims to distinguish invasive (blood stream
infection) and non-invasive (nasal colonization) MRSA isolates of
the same CC5 into phylogenetic- and virulence-associated
genotypic subgroups by WGS and MA. A cohort of twelve blood
stream and fifteen nasal MRSA isolates of CC5 (spa-types t003 and
t504) was selected. Isolates were propagated at the same period
of time from unrelated patients treated at the University of
Saarland Medical Center, Germany. Rooted phylotyping based on WGS
with core-genome single nucleotide polymorphism (SNP) analysis
revealed two local clusters of closely related CC5 subgroups
(t504 and Clade1 t003) which were separated from other local t003
isolates and from unrelated CC5 MRSA reference isolates of German
origin. Phylogenetic subtyping was not associated with
invasiveness when comparing blood stream and nasal isolates.
Clustering based on MA profiles was not concordant with WGS
phylotyping, but MA profiles may identify subgroups of isolates
with nasal and blood stream origin. Among the new putative
virulence associated genes identified by WGS, the strongest
association with blood stream infections was shown for ebhB
mutants. Analysis of the core-genome together with the accessory
genome enables subtyping of closely related MRSA isolates
according to phylogeny and presumably also to the potential
virulence capacity of isolates.",
journal = "Infect. Genet. Evol.",
volume = 36,
pages = "475--482",
month = dec,
year = 2015,
keywords = "DNA microarray; Invasiveness; MRSA; Phylogeny; Staphylococcus
aureus; Whole genome
sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Steinig2015-si,
title = "Single-molecule sequencing reveals the molecular basis of
multidrug-resistance in {ST772} methicillin-resistant
Staphylococcus aureus",
author = "Steinig, Eike J and Andersson, Patiyan and Harris, Simon R and
Sarovich, Derek S and Manoharan, Anand and Coupland, Paul and
Holden, Matthew T G and Parkhill, Julian and Bentley, Stephen D
and Robinson, D Ashley and Tong, Steven Y C",
abstract = "BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is
a major cause of hospital-associated infection, but there is
growing awareness of the emergence of multidrug-resistant
lineages in community settings around the world. One such lineage
is ST772-MRSA-V, which has disseminated globally and is
increasingly prevalent in India. Here, we present the complete
genome sequence of DAR4145, a strain of the ST772-MRSA-V lineage
from India, and investigate its genomic characteristics in
regards to antibiotic resistance and virulence factors. RESULTS:
Sequencing using single-molecule real-time technology resulted in
the assembly of a single continuous chromosomal sequence, which
was error-corrected, annotated and compared to nine draft genome
assemblies of ST772-MRSA-V from Australia, Malaysia and India. We
discovered numerous and redundant resistance genes associated
with mobile genetic elements (MGEs) and known core genome
mutations that explain the highly antibiotic resistant phenotype
of DAR4145. Staphylococcal toxins and superantigens, including
the leukotoxin Panton-Valentinin Leukocidin, were predominantly
associated with genomic islands and the phage
$\varphi$-IND772PVL. Some of these mobile resistance and
virulence factors were variably present in other strains of the
ST772-MRSA-V lineage. CONCLUSIONS: The genomic characteristics
presented here emphasize the contribution of MGEs to the
emergence of multidrug-resistant and highly virulent strains of
community-associated MRSA. Antibiotic resistance was further
augmented by chromosomal mutations and redundancy of resistance
genes. The complete genome of DAR4145 provides a valuable
resource for future investigations into the global dissemination
and phylogeography of ST772-MRSA-V.",
journal = "BMC Genomics",
volume = 16,
pages = "388",
month = may,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Stipetic2015-tc,
title = "Draft Genome Sequence of Isolate Staphylococcus aureus
{LHSKBClinical}, Isolated from an Infected Hip",
author = "Stipetic, Laurence H and Hamilton, Graham and Dalby, Matthew J
and Davies, Robert L and Meek, R M Dominic and Ramage, Gordon and
Smith, David G E and Burgess, Karl E V",
abstract = "We report here the genome sequence of a clinical isolate of
Staphylococcus aureus from an orthopedic infection.
Phenotypically diverse Staphylococcus aureus strains are
associated with orthopedic infections and subsequent implant
failure, and some are highly resistant to antibiotics. This
genome sequence will support further analyses of strains causing
orthopedic infections.",
journal = "Genome Announc.",
volume = 3,
number = 2,
month = apr,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Cazares-Dominguez2015-re,
title = "Vancomycin tolerant, methicillin-resistant Staphylococcus aureus
reveals the effects of vancomycin on cell wall thickening",
author = "C{\'a}zares-Dom{\'\i}nguez, Vicenta and Cruz-C{\'o}rdova,
Ariadnna and Ochoa, Sara A and Escalona, Gerardo and
Arellano-Galindo, Jos{\'e} and Rodr{\'\i}guez-Leviz, Alejandra
and Hern{\'a}ndez-Castro, Rigoberto and L{\'o}pez-Villegas, Edgar
O and Xicohtencatl-Cortes, Juan",
abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) is an
important opportunistic pathogen that causes both healthcare- and
community-acquired infections. An increase in the incidence of
these infections may lead to a substantial change in the rate of
vancomycin usage. Incidence of reduced susceptibility to
vancomycin has been increasing worldwide for the last few years,
conferring different levels of resistance to vancomycin as well
as producing changes in the cell wall structure. The aim of the
present study was to determine the effect of vancomycin on cell
wall thickening in clinical isolates of vancomycin-tolerant (VT)
MRSA obtained from pediatric patients. From a collection of 100
MRSA clinical isolates from pediatric patients, 12\% (12/100)
were characterized as VT-MRSA, and from them, 41.66\% (5/12)
exhibited the heterogeneous vancomycin-intermediate S. aureus
(hVISA) phenotype. Multiplex-PCR assays revealed 66.66\% (8/12),
25\% (3/12), and 8.33\% (1/12) of the VT-MRSA isolates were
associated with agr group II, I, and III polymorphisms,
respectively; the II-mec gene was amplified from 83.3\% (10/12)
of the isolates, and the mecIVa gene was amplified from 16.66\%
(2/12) of the isolates. Pulsed field electrophoresis (PFGE)
fingerprint analysis showed 62\% similarity among the VT-MRSA
isolates. Thin transverse sections analyzed by transmission
electron microscopy (TEM) revealed an average increase of 24 nm
(105.55\%) in the cell wall thickness of VT-MRSA compared with
untreated VT-MRSA isolates. In summary, these data revealed that
the thickened cell walls of VT-MRSA clinical isolates with agr
type II and SCCmec group II polymorphisms are associated with an
adaptive resistance to vancomycin.",
journal = "PLoS One",
volume = 10,
number = 3,
pages = "e0118791",
month = mar,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Yamaguchi2015-vn,
title = "Evolution and single-nucleotide polymorphisms in
methicillin-resistant Staphylococcus aureus strains with reduced
susceptibility to vancomycin and daptomycin, based on
determination of the complete genome",
author = "Yamaguchi, Tetsuo and Suzuki, Shingo and Okamura, Sakiko and
Miura, Yuri and Tsukimori, Ayaka and Nakamura, Itaru and Ito,
Norihiko and Masuya, Anri and Shiina, Takashi and Matsumoto,
Tetsuya",
abstract = "We obtained a series of methicillin-resistant Staphylococcus
aureus isolates, including both daptomycin-susceptible strain TD1
and daptomycin-resistant strain TD4, from a patient. We
determined the complete genome sequences of TD1 and TD4 using
next-generation sequencing, and only four single-nucleotide
polymorphisms (SNPs) were identified, one each in capB (E58K),
rpoB (H481Y), lytN (I16V), and mprF (V351E). We determined that
these four SNPs were sufficient to cause the strains to develop
daptomycin, vancomycin, and rifampin resistance.",
journal = "Antimicrob. Agents Chemother.",
volume = 59,
number = 6,
pages = "3585--3587",
month = mar,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Daum2015-li,
title = "{Whole-Genome} Sequence for {Methicillin-Resistant}
Staphylococcus aureus Strain {ATCC} {BAA-1680}",
author = "Daum, Luke T and Bumah, Violet V and Masson-Meyers, Daniela S and
Khubbar, Manjeet and Rodriguez, John D and Fischer, Gerald W and
Enwemeka, Chukuka S and Gradus, Steve and Bhattacharyya, Sanjib",
abstract = "We report here the whole-genome sequence of the USA300 strain of
methicillin-resistant Staphylococcus aureus (MRSA), designated
ATCC BAA-1680, and commonly referred to as community-associated
MRSA (CA-MRSA). This clinical MRSA isolate is commercially
available from the American Type Culture Collection (ATCC) and is
widely utilized as a control strain for research applications and
clinical diagnosis. The isolate was propagated in ATCC medium 18,
tryptic soy agar, and has been utilized as a model S. aureus
strain in several studies, including MRSA genetic analysis after
irradiation with 470-nm blue light.",
journal = "Genome Announc.",
volume = 3,
number = 2,
month = mar,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Anderson2014-qt,
title = "Whole Genome Sequencing of a {Methicillin-Resistant}
Staphylococcus aureus {Pseudo-Outbreak} in a Professional
Football Team",
author = "Anderson, Deverick J and Harris, Simon R and Godofsky, Eliot and
Toriscelli, Todd and Rude, Thomas H and Elder, Kevin and Sexton,
Daniel J and Pellman, Elliot J and Mayer, Thom and Fowler, Jr,
Vance G and Peacock, Sharon J",
abstract = "Two American football players on the same team were diagnosed
with methicillin-resistant Staphylococcus aureus (MRSA) skin and
soft tissue infections on the same day. Our investigation,
including whole genome sequencing, confirmed that players did not
transmit MRSA to one another nor did they acquire the MRSA from a
single source within the training facility.",
journal = "Open Forum Infect Dis",
volume = 1,
number = 3,
pages = "ofu096",
month = dec,
year = 2014,
keywords = "American football; MRSA; outbreak investigation; whole genome
sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Hattangady2015-we,
title = "Genomic, Transcriptomic and Metabolomic Studies of Two
{Well-Characterized}, {Laboratory-Derived}
{Vancomycin-Intermediate} Staphylococcus aureus Strains Derived
from the Same Parent Strain",
author = "Hattangady, Dipti S and Singh, Atul K and Muthaiyan, Arun and
Jayaswal, Radheshyam K and Gustafson, John E and Ulanov,
Alexander V and Li, Zhong and Wilkinson, Brian J and Pfeltz,
Richard F",
abstract = "Complete genome comparisons, transcriptomic and metabolomic
studies were performed on two laboratory-selected,
well-characterized vancomycin-intermediate Staphylococcus aureus
(VISA) derived from the same parent MRSA that have changes in
cell wall composition and decreased autolysis. A variety of
mutations were found in the VISA, with more in strain
13136p(-)m⁺V20 (vancomycin MIC = 16 µg/mL) than strain
13136p(-)m⁺V5 (MIC = 8 µg/mL). Most of the mutations have not
previously been associated with the VISA phenotype; some were
associated with cell wall metabolism and many with stress
responses, notably relating to DNA damage. The genomes and
transcriptomes of the two VISA support the importance of gene
expression regulation to the VISA phenotype. Similarities in
overall transcriptomic and metabolomic data indicated that the
VISA physiologic state includes elements of the stringent
response, such as downregulation of protein and nucleotide
synthesis, the pentose phosphate pathway and nutrient transport
systems. Gene expression for secreted virulence determinants was
generally downregulated, but was more variable for
surface-associated virulence determinants, although capsule
formation was clearly inhibited. The importance of activated
stress response elements could be seen across all three analyses,
as in the accumulation of osmoprotectant metabolites such as
proline and glutamate. Concentrations of potential cell wall
precursor amino acids and glucosamine were increased in the VISA
strains. Polyamines were decreased in the VISA, which may
facilitate the accrual of mutations. Overall, the studies confirm
the wide variability in mutations and gene expression patterns
that can lead to the VISA phenotype.",
journal = "Antibiotics (Basel)",
volume = 4,
number = 1,
pages = "76--112",
month = feb,
year = 2015,
keywords = "Staphylococcus aureus; VISA; genomics; metabolomics;
transcriptomics;Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Fluit2015-cw,
title = "Comparison of an {ST80} {MRSA} strain from the {USA} with
European {ST80} strains",
author = "Fluit, Ad C and Carpaij, Neeltje and Majoor, Eline A M and
Weinstein, Robert A and Aroutcheva, Alla and Rice, Thomas W and
Bonten, Marc J M and Willems, Rob J L",
abstract = "OBJECTIVES: A number of community-acquired MRSA (CA-MRSA) clonal
lineages dominate worldwide. ST80 was dominant in Europe and has
increasingly been described from the Middle East. Here we report
the whole genome sequence of the first ST80 CA-MRSA from the USA.
METHODS: CA-MRSA isolate S0924 was obtained from a patient
admitted to Cook County Hospital (Chicago, IL, USA) who came from
Syria; the isolate belonged to spa type t044 and ST80. The whole
genome sequence of S0924 was determined and compared with three
previously published whole genome sequences of ST80 CA-MRSA from
Europe and a newly sequenced ST80 CA-MRSA from the Netherlands
(S1475). RESULTS: Based on spa typing, SCCmec type and virulence
gene profile, this US ST80 isolate is indistinguishable from the
European CA-MRSA ST80 clone. SNP analysis within the conserved
core genome showed clear differences between the strains with up
to 144 SNPs differing between S0924 and strain S1800, an ST80
MRSA from Greece. The gene content showed 21 regions of
difference between the US and European isolates, although these
were largely restricted to mobile genetic elements. Phylogenetic
reconstruction indicated that the European strains were more
closely related to each other than to the US strain. The SNP data
suggest that a common ancestor existed around two decades ago,
indicating that the US and European ST80 strains are clonally
linked. CONCLUSIONS: These data combined with the country of
origin of the patient suggest that ST80 S0924 was probably
relatively recently introduced into the USA from Syria.",
journal = "J. Antimicrob. Chemother.",
volume = 70,
number = 3,
pages = "664--669",
month = mar,
year = 2015,
keywords = "CA-MRSA; US; whole genome
sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Guo2015-yz,
title = "Use of genome sequencing to assess nucleotide structure variation
of Staphylococcus aureus strains cultured in spaceflight on
{Shenzhou-X}, under simulated microgravity and on the ground",
author = "Guo, Jun and Han, Na and Zhang, Yuanyuan and Wang, Haiyin and
Zhang, Xuelin and Su, Longxiang and Liu, Chao and Li, Jia and
Chen, Chen and Liu, Changting",
abstract = "The extreme environment of space could affect microbial behavior
and may increase the risk of infectious disease during
spaceflight. However, the molecular genetic changes of
methicillin-resistant Staphylococcus aureus (MRSA) in response to
the spaceflight environment have not been fully clarified. In the
present study, we determined the draft genome sequences for an
ancestral S. aureus strain (LCT-SAO) isolated from a clinical
sample and three derivative strains, LCT-SAS, LCT-SAM and
LCT-SAG, cultured in parallel during the spaceflight Shenzhou-X,
under simulated microgravity and on the ground, respectively. To
evaluate the impact of short-term spaceflight on the MRSA
strains, comparative genomic analysis was implemented.
Genome-based mapping of toxin genes and antibiotic resistance
genes confirmed that these strains have the conventional
pathogenicity and resistance to drugs, as none of the strains
showed significant changes in these regions after culturing in
the three different environments; this result suggests that
spaceflight may not change bacterial virulence or drug
resistance. Thirty-nine strain-specific sequence variants (SVs)
were identified throughout the genomes, and the three derivatives
exhibited almost the same mutation rates. Fifty-nine percent of
SVs were located in the intergenic regions of the genomes,
indicating that S. aureus may have an extremely robust repair
mechanism responsible for recognizing and repairing DNA
replication mismatches. It is noteworthy that strain LCT-SAS,
cultured in space, presented the most unique SVs (n=9) and shared
the fewest SVs with LCT-SAM (n=5) and LCT-SAG (n=4). Furthermore,
we identified 10 potential deletion regions and 2 potential
insertion regions, with LCT-SAS appearing more fragile than other
strains by this measure. These results suggest that the
environment of space is inherently complicated, with multiple
variables, and cannot be simulated in a simple manner. Our
results represent the first analysis of nucleotide structure
variation of S. aureus strains in a spaceflight environment and
also provide a valuable insight for understanding the mutation
strategies of MRSA on earth.",
journal = "Microbiol. Res.",
volume = 170,
pages = "61--68",
month = jan,
year = 2015,
keywords = "Genome; High-throughput; SNP; Spaceflight; Staphylococcus
aureus;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Ramaraj2014-yk,
title = "Draft Genome Sequences of {Vancomycin-Susceptible} Staphylococcus
aureus Related to Heterogeneous {Vancomycin-Intermediate} S.
aureus",
author = "Ramaraj, Thiruvarangan and Matyi, Stephanie A and Sundararajan,
Anitha and Lindquist, Ingrid E and Devitt, Nicolas P and
Schilkey, Faye D and Lamichhane-Khadka, Reena and Hoyt, Peter R
and Mudge, Joann and Gustafson, John E",
abstract = "We report the draft genome sequences of three
vancomycin-susceptible methicillin-resistant Staphylococcus
aureus strains. S. aureus strain MV8 is a sequence type 8 (ST-8)
staphylococcal cassette chromosome mec element type IV (SCCmec
IV) derivative, while the other two strains (S. aureus MM25 and
MM61) are ST-5 SCCmec II strains. MM61 is also closely related to
the heterogeneous vancomycin-intermediate S. aureus strain MM66.",
journal = "Genome Announc.",
volume = 2,
number = 5,
month = oct,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Kropp2014-ci,
title = "Draft Genome Sequence of a Staphylococcus aureus Isolate Taken
from the Blood of a Preterm Neonatal Blood Sepsis Patient",
author = "Kropp, K A and Lucid, A and Carroll, J and Belgrudov, V and
Walsh, P and Kelly, B and Templeton, K and Smith, C and
Dickinson, P and O'Driscoll, A and Ghazal, P and Sleator, R D",
abstract = "Herein, we report the draft genome sequence of Staphylococcus
aureus ED-NGS-1006, cultivated from a blood sample taken from a
neonatal sepsis patient at the Royal Infirmary in Edinburgh,
Scotland, United Kingdom.",
journal = "Genome Announc.",
volume = 2,
number = 5,
month = sep,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Stegger2014-wr,
title = "Origin and evolution of European community-acquired
methicillin-resistant Staphylococcus aureus",
author = "Stegger, Marc and Wirth, Thierry and Andersen, Paal S and Skov,
Robert L and De Grassi, Anna and Sim{\~o}es, Patricia Martins and
Tristan, Anne and Petersen, Andreas and Aziz, Maliha and Kiil,
Kristoffer and Cirkovi{\'c}, Ivana and Udo, Edet E and del Campo,
Rosa and Vuopio-Varkila, Jaana and Ahmad, Norazah and Tokajian,
Sima and Peters, Georg and Schaumburg, Frieder and
Olsson-Liljequist, Barbro and Givskov, Michael and Driebe,
Elizabeth E and Vigh, Henrik E and Shittu, Adebayo and
Ramdani-Bougessa, Nadjia and Rasigade, Jean-Philippe and Price,
Lance B and Vandenesch, Francois and Larsen, Anders R and
Laurent, Frederic",
abstract = "UNLABELLED: Community-acquired methicillin-resistant
Staphylococcus aureus (CA-MRSA) was recognized in Europe and
worldwide in the late 1990s. Within a decade, several genetically
and geographically distinct CA-MRSA lineages carrying the small
SCCmec type IV and V genetic elements and the Panton-Valentine
leukocidin (PVL) emerged around the world. In Europe, the
predominant CA-MRSA strain belongs to clonal complex 80 (CC80)
and is resistant to kanamycin/amikacin and fusidic acid. CC80 was
first reported in 1993 but was relatively rare until the late
1990s. It has since been identified throughout North Africa, the
Middle East, and Europe, with recent sporadic reports in
sub-Saharan Africa. While strongly associated with skin and soft
tissue infections, it is rarely found among asymptomatic
carriers. Methicillin-sensitive S. aureus (MSSA) CC80 strains are
extremely rare except in sub-Saharan Africa. In the current
study, we applied whole-genome sequencing to a global collection
of both MSSA and MRSA CC80 isolates. Phylogenetic analyses
strongly suggest that the European epidemic CA-MRSA lineage is
derived from a PVL-positive MSSA ancestor from sub-Saharan
Africa. Moreover, the tree topology suggests a single acquisition
of both the SCCmec element and a plasmid encoding the fusidic
acid resistance determinant. Four canonical SNPs distinguish the
derived CA-MRSA lineage and include a nonsynonymous mutation in
accessory gene regulator C (agrC). These changes were associated
with a star-like expansion into Europe, the Middle East, and
North Africa in the early 1990s, including multiple cases of
cross-continent imports likely driven by human migrations.
IMPORTANCE: With increasing levels of CA-MRSA reported from most
parts of the Western world, there is a great interest in
understanding the origin and factors associated with the
emergence of these epidemic lineages. To trace the origin,
evolution, and dissemination pattern of the European CA-MRSA
clone (CC80), we sequenced a global collection of strains of the
S. aureus CC80 lineage. Our study determined that a single
descendant of a PVL-positive methicillin-sensitive ancestor
circulating in sub-Saharan Africa rose to become the dominant
CA-MRSA clone in Europe, the Middle East, and North Africa. In
the transition from a methicillin-susceptible lineage to a
successful CA-MRSA clone, it simultaneously became resistant to
fusidic acid, a widely used antibiotic for skin and soft tissue
infections, thus demonstrating the importance of antibiotic
selection in the success of this clone. This finding furthermore
highlights the significance of horizontal gene acquisitions and
underscores the combined importance of these factors for the
success of CA-MRSA.",
journal = "MBio",
volume = 5,
number = 5,
pages = "e01044--14",
month = aug,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Matyi2014-ug,
title = "Draft Genomes of Heterogeneous {Vancomycin-Intermediate}
Staphylococcus aureus Strain {MM66} and {MM66} Derivatives with
Altered Vancomycin Resistance Levels",
author = "Matyi, Stephanie A and Ramaraj, Thiruvarangan and Sundararajan,
Anitha and Lindquist, Ingrid E and Devitt, Nicolas P and
Schilkey, Faye D and Lamichhane-Khadka, Reena and Hoyt, Peter R
and Mudge, Joann and Gustafson, John E",
abstract = "The draft genomes of heterogeneous vancomycin-intermediate
Staphylococcus aureus (hVISA) strain MM66 and MM66 isolates
demonstrating altered vancomycin resistance levels were produced
in an effort to provide information on mutations contributing to
the vancomycin resistance levels observed in these strains.",
journal = "Genome Announc.",
volume = 2,
number = 4,
month = jul,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Jeon2014-nu,
title = "Complete Genome Sequence of the Siphoviral Bacteriophage
{YMC/09/04/R1988} {MRSA} {BP}: A lytic phage from a
methicillin-resistant Staphylococcus aureus isolate",
author = "Jeon, Jongsoo and D'Souza, Roshan and Hong, Sung Kuk and Lee,
Yangsoon and Yong, Dongeun and Choi, Jongrak and Lee, Kyungwon
and Chong, Yunsop",
abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) is an
increasing cause of serious infection, both in the community and
hospital settings. Despite sophisticated strategies and efforts,
the antibiotic options for treating MRSA infection have been
narrowed due to the limited number of newly developed
antimicrobials. Herein, we analyze the completely sequenced
genome of a novel virulent phage YMC/09/04/R1988 MRSA BP as a
potential alternative anti-MRSA agent, which lysed clinical
isolates from a patient admitted to the hospital due to hip
disarticulation. The phage contains a linear double-stranded DNA
genome of 44,459 bp in length, with 33.37\% GC content, 62
predicted open reading frames (ORFs), and annotated functions of
only 23 ORFs that are associated with structural assembly, host
lysis, DNA replication, and modification. It showed a broad host
range (17 of 30 strains) against MRSA strains in clinical
isolates. This article is protected by copyright. All rights
reserved.",
journal = "FEMS Microbiol. Lett.",
month = aug,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Keary2014-ke,
title = "Genome analysis of the staphylococcal temperate phage {DW2} and
functional studies on the endolysin and tail hydrolase",
author = "Keary, Ruth and McAuliffe, Olivia and Ross, R Paul and Hill,
Colin and O'Mahony, Jim and Coffey, Aidan",
abstract = "This study describes the genome of temperate Siphoviridae phage
DW2, which is routinely propagated on Staphylococcus aureus
DPC5246. The 41941 bp genome revealed an open reading frame
(ORF1) which has a high level of homology with members of the
resolvase subfamily of site-specific serine recombinase, involved
in chromosomal integration and excision. In contrast, the
majority of staphylococcal phages reported to date encode
tyrosine recombinases. Two putative genes encoded by phage DW2
(ORF15 and ORF24) were highly homologous to the NWMN0273 and
NWMN0280 genes encoding virulence factors carried on the genome
of ϕNM4, a prophage in the genome of S. aureus Newman. Phage DW2
also encodes proteins highly homologous to two well-characterized
Staphylococcus aureus pathogenicity island derepressors encoded
by the staphylococcal helper phage 80$\alpha$ indicating that it
may similarly act as a helper phage for mobility of pathogenicity
islands in S. aureus. This study also focused on the enzybiotic
potential of phage DW2. The structure of the putative endolysin
and tail hydrolase were investigated and used as the basis for a
cloning strategy to create recombinant peptidoglycan hydrolyzing
proteins. After overexpression in E. coli, four of these proteins
(LysDW2, THDW2, CHAPE1-153, and CHAPE1-163) were demonstrated to
have hydrolytic activity against peptidoglycan of S. aureus and
thus represent novel candidates for exploitation as enzybiotics.",
journal = "Bacteriophage",
volume = 4,
pages = "e28451",
month = mar,
year = 2014,
keywords = "Staphylococcus; bacteriophage; endolysin; serine recombinase;
virion-associated peptidoglycan hydrolase;
virulence;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{SenGupta2014-is,
title = "Whole-genome sequencing for high-resolution investigation of
methicillin-resistant Staphylococcus aureus epidemiology and
genome plasticity",
author = "SenGupta, Dhruba J and Cummings, Lisa A and Hoogestraat, Daniel R
and Butler-Wu, Susan M and Shendure, Jay and Cookson, Brad T and
Salipante, Stephen J",
abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) infections
pose a major challenge in health care, yet the limited
heterogeneity within this group hinders molecular investigations
of related outbreaks. Pulsed-field gel electrophoresis (PFGE) has
been the gold standard approach but is impractical for many
clinical laboratories and is often replaced with PCR-based
methods. Regardless, both approaches can prove problematic for
identifying subclonal outbreaks. Here, we explore the use of
whole-genome sequencing for clinical laboratory investigations of
MRSA molecular epidemiology. We examine the relationships of 44
MRSA isolates collected over a period of 3 years by using
whole-genome sequencing and two PCR-based methods, multilocus
variable-number tandem-repeat analysis (MLVA) and spa typing. We
find that MLVA offers higher resolution than spa typing, as it
resolved 17 versus 12 discrete isolate groups, respectively. In
contrast, whole-genome sequencing reproducibly cataloged genomic
variants (131,424 different single nucleotide polymorphisms and
indels across the strain collection) that uniquely identified
each MRSA clone, recapitulating those groups but enabling
higher-resolution phylogenetic inferences of the epidemiological
relationships. Importantly, whole-genome sequencing detected a
significant number of variants, thereby distinguishing between
groups that were considered identical by both spa typing
(minimum, 1,124 polymorphisms) and MLVA (minimum, 193
polymorphisms); this suggests that these more conventional
approaches can lead to false-positive identification of outbreaks
due to inappropriate grouping of genetically distinct strains. An
analysis of the distribution of variants across the MRSA genome
reveals 47 mutational hot spots (comprising ∼ 2.5\% of the
genome) that account for 23.5\% of the observed polymorphisms,
and the use of this selected data set successfully recapitulates
most epidemiological relationships in this pathogen group.",
journal = "J. Clin. Microbiol.",
volume = 52,
number = 8,
pages = "2787--2796",
month = aug,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Dordel2014-pp,
title = "Novel determinants of antibiotic resistance: identification of
mutated loci in highly methicillin-resistant subpopulations of
methicillin-resistant Staphylococcus aureus",
author = "Dordel, Janina and Kim, Choonkeun and Chung, Marilyn and Pardos
de la G{\'a}ndara, Mar{\'\i}a and Holden, Matthew T J and
Parkhill, Julian and de Lencastre, Herm{\'\i}nia and Bentley,
Stephen D and Tomasz, Alexander",
abstract = "We identified mutated genes in highly resistant subpopulations of
methicillin-resistant Staphylococcus aureus (MRSA) that are most
likely responsible for the historic failure of the $\beta$-lactam
family of antibiotics as therapeutic agents against these
important pathogens. Such subpopulations are produced during
growth of most clinical MRSA strains, including the four
historically early MRSA isolates studied here. Chromosomal DNA
was prepared from the highly resistant cells along with DNA from
the majority of cells (poorly resistant cells) followed by full
genome sequencing. In the highly resistant cells, mutations were
identified in 3 intergenic sequences and 27 genes representing a
wide range of functional categories. A common feature of these
mutations appears to be their capacity to induce high-level
$\beta$-lactam resistance and increased amounts of the resistance
protein PBP2A in the bacteria. The observations fit a recently
described model in which the ultimate controlling factor of the
phenotypic expression of $\beta$-lactam resistance in MRSA is a
RelA-mediated stringent response. IMPORTANCE It has been well
established that the level of antibiotic resistance (i.e.,
minimum concentration of a $\beta$-lactam antibiotic needed to
inhibit growth) of a methicillin-resistant Staphylococcus aureus
(MRSA) strain depends on the transcription and translation of the
resistance protein PBP2A. Here we describe mutated loci in an
additional novel set of genetic determinants that appear to be
essential for the unusually high resistance levels typical of
subpopulations of staphylococci that are produced with unique low
frequency in most MRSA clinical isolates. We propose that
mutations in these determinants can trigger induction of the
stringent stress response which was recently shown to cause
increased transcription/translation of the resistance protein
PBP2A in parallel with the increased level of resistance.",
journal = "MBio",
volume = 5,
number = 2,
pages = "e01000",
month = apr,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Baines2015-ms,
title = "Convergent Adaptation in the Dominant Global Hospital Clone
{ST239} of {Methicillin-Resistant} Staphylococcus aureus",
author = "Baines, Sarah L and Holt, Kathryn E and Schultz, Mark B and
Seemann, Torsten and Howden, Brian O and Jensen, Slade O and van
Hal, Sebastiaan J and Coombs, Geoffrey W and Firth, Neville and
Powell, David R and Stinear, Timothy P and Howden, Benjamin P",
abstract = "UNLABELLED: Infections caused by highly successful clones of
hospital-associated methicillin-resistant Staphylococcus aureus
(HA-MRSA) are a major public health burden. The globally dominant
sequence type 239 (ST239) HA-MRSA clone has persisted in the
health care setting for decades, but the basis of its success has
not been identified. Taking a collection of 123 ST239 isolates
spanning 32 years, we have used population-based functional
genomics to investigate the evolution of this highly persistent
and successful clone. Phylogenetic reconstruction and population
modeling uncovered a previously unrecognized distinct clade of
ST239 that was introduced into Australia from Asia and has
perpetuated the epidemic in this region. Functional analysis
demonstrated attenuated virulence and enhanced resistance to
last-line antimicrobials, the result of two different phenomena,
adaptive evolution within the original Australian ST239 clade and
the introduction of a new clade displaying shifts in both
phenotypes. The genetic diversity between the clades allowed us
to employ genome-wide association testing and identify mutations
in other essential regulatory systems, including walKR, that
significantly associate with and may explain these key
phenotypes. The phenotypic convergence of two independently
evolving ST239 clades highlights the very strong selective
pressures acting on HA-MRSA, showing that hospital environments
have favored the accumulation of mutations in essential MRSA
genes that increase resistance to antimicrobials, attenuate
virulence, and promote persistence in the health care
environment. Combinations of comparative genomics and careful
phenotypic measurements of longitudinal collections of clinical
isolates are giving us the knowledge to intelligently address the
impact of current and future antibiotic usage policies and
practices on hospital pathogens globally. IMPORTANCE:
Methicillin-resistant Staphylococcus aureus (MRSA) is responsible
for innumerable drug-resistant health care-associated infections
globally. This study, the first to investigate the evolutionary
response of hospital-associated MRSA (HA-MRSA) over many decades,
demonstrates how MRSA can persist in a region through the
reintroduction of a previously unrecognized distinct clade. This
study also demonstrates the crucial adaptive responses of HA-MRSA
to the highly selective environment of the health care system,
the evolution of MRSA isolates to even higher levels of
antibiotic resistance at the cost of attenuated virulence.
However, in vivo persistence is maintained, resulting in a clone
of HA-MRSA able to resist almost all antimicrobial agents and
still cause invasive disease in the heavily compromised hosts
found in modern health care settings.",
journal = "MBio",
volume = 6,
number = 2,
pages = "e00080",
month = may,
year = 2015,
keywords = "Staphylococcus;Staph\_evolutionary\_history;bacterial comparative
genomics;antibiotcs-evolution-fitness;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;GWAS-bacteria"
}
@ARTICLE{Qu2014-cf,
title = "Whole genome analysis of a community-associated
methicillin-resistant Staphylococcus aureus {ST59} isolate from a
case of human sepsis and severe pneumonia in China",
author = "Qu, Tingting and Feng, Ye and Jiang, Yan and Zhu, Peiqiong and
Wei, Zeqing and Chen, Yan and Otto, Michael and Yu, Yunsong",
abstract = "We report a case of necrotizing pneumonia in a young patient
caused by community acquired-methicillin resistant Staphylococcus
aureus (CA-MRSA) in a teaching hospital in the People's Republic
of China. The patient had a typical clinical presentation and was
successfully treated with antibiotics and intravenous
immunoglobulin. A CA-MRSA strain, named SA268, was isolated from
the blood of the patient. The isolate was susceptible to most
antimicrobial agents, except cephalosporins, penicillins, and
$\beta$-lactamase inhibitor combinations. Multi-locus sequence
typing (MLST) assigned SA268 to ST59, a clone widely spread in
eastern Asia. The strain was positive for Panton Valentine
Leukocidin (PVL)-encoding genes and SCCmec type V. We sequenced
the complete genome of the SA268 isolate. The genome of SA268 was
almost identical to that of the Taiwanese ST59 CA-MRSA strains
M013 and SA957. However, we observed several differences in gene
composition, which included differences in the SCCmec element and
several lipoprotein genes that were present in the Taiwanese
strains but absent from SA268.",
journal = "PLoS One",
volume = 9,
number = 2,
pages = "e89235",
month = feb,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Elbir2013-tl,
title = "Staphylococcus aureus subsp. anaerobius strain {ST1464} genome
sequence",
author = "Elbir, Haitham and Robert, Catherine and Nguyen, Ti Thien and
Gimenez, Gr{\'e}gory and El Sanousi, Sulieman M and Flock,
Jan-Ingmar and Raoult, Didier and Drancourt, Michel",
abstract = "Staphylococcus aureus subsp. anaerobius is responsible for
Morel's disease in animals and a cause of abscess in humans. It
is characterized by a microaerophilic growth, contrary to the
other strains of S. aureus. The 2,604,446-bp genome (32.7\% GC
content) of S. anaerobius ST1464 comprises one chromosome and no
plasmids. The chromosome contains 2,660 open reading frames
(ORFs), 49 tRNAs and three complete rRNAs, forming one complete
operon. The size of ORFs ranges between 100 to 4,600 bp except
for two ORFs of 6,417 and 7,173 bp encoding segregation ATPase
and non-ribosomal peptide synthase, respectively. The chromosome
harbors Staphylococcus phage 2638A genome and incomplete
Staphylococcus phage genome PT1028, but no detectable CRISPRS.
The antibiotic resistance gene for tetracycline was found
although Staphylococcus aureus subsp. anaerobius is susceptible
to tetracycline in-vitro. Intact oxygen detoxification genes
encode superoxide dismutase and cytochrome quinol oxidase whereas
the catalase gene is impaired by a stop codon. Based on the
genome, in-silico multilocus sequence typing indicates that S.
aureus subsp. anaerobius emerged as a clone separated from all
other S. aureus strains, illustrating host-adaptation linked to
missing functions. Availability of S. aureus subsp. anaerobius
genome could prompt the development of post-genomic tools for its
rapid discrimination from S. aureus.",
journal = "Stand. Genomic Sci.",
volume = 9,
number = 1,
pages = "1--13",
month = oct,
year = 2013,
keywords = "Morel's disease; SOLiD; Staphylococcus aureus subsp. anaerobius;
genome;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Monecke2013-fe,
title = "Genome sequencing and molecular characterisation of
Staphylococcus aureus {ST772-MRSA-V}, ``Bengal Bay Clone''",
author = "Monecke, Stefan and Baier, Vico and Coombs, Geoffrey W and
Slickers, Peter and Ziegler, Albrecht and Ehricht, Ralf",
abstract = "BACKGROUND: The PVL-positive ST772-MRSA-V is an emerging
community-associated (CA-) MRSA clone that has been named Bengal
Bay Clone since most patients have epidemiological connections to
the Indian subcontinent. It is found increasingly common in other
areas of the world. METHODS: One isolate of ST772-MRSA-V was
sequenced using the Illumina Genome Analyzer System. After
initial assembling the multiple sequence contigs were analysed
using different in-house annotation scripts. Results were
compared to microarray hybridisation results of clinical isolates
of ST772-MRSA-V, of related strains and to another ST772-MRSA-V
genome sequence. RESULTS: According to MLST e-burst analysis,
ST772-MRSA-V belongs to Clonal Complex (CC)1, differing from ST1
only in one MLST allele (pta-22). However, there are several
additional differences including agr alleles (group II rather
than III), capsule type (5 rather than 8), the presence of the
egc enterotoxin gene cluster and of the enterotoxin homologue ORF
CM14 as well as the absence of the enterotoxin H gene seh.
Enterotoxin genes sec and sel are present. ST772-MRSA-V harbours
the genes encoding enterotoxin A (sea) and PVL (lukS/F-PV). Both
are located on the same prophage. CONCLUSIONS: ST772-MRSA-V may
have emerged from the same lineage as globally spread CC1 and CC5
strains. It has acquired a variety of virulence factors, and for
a CA-MRSA strain it has an unusually high number of genes
associated with antibiotic resistance.",
journal = "BMC Res. Notes",
volume = 6,
pages = "548",
month = dec,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Baek2013-yj,
title = "Genetic variation in the Staphylococcus aureus 8325 strain
lineage revealed by whole-genome sequencing",
author = "B{\ae}k, Kristoffer T and Frees, Dorte and Renzoni, Adriana and
Barras, Christine and Rodriguez, Natalia and Manzano, Caroline
and Kelley, William L",
abstract = "Staphylococcus aureus strains of the 8325 lineage, especially
8325-4 and derivatives lacking prophage, have been used
extensively for decades of research. We report herein the results
of our deep sequence analysis of strain 8325-4. Assignment of
sequence variants compared with the reference strain 8325
(NRS77/PS47) required correction of errors in the 8325 reference
genome, and reassessment of variation previously attributed to
chemical mutagenesis of the restriction-defective RN4220. Using
an extensive strain pedigree analysis, we discovered that 8325-4
contains 16 single nucleotide polymorphisms (SNP) arising prior
to the construction of RN4220. We identified 5 indels in 8325-4
compared with 8325. Three indels correspond to expected $\Phi$11,
12, 13 excisions, one indel is explained by a sequence assembly
artifact, and the final indel ($\Delta$63bp) in the spa-sarS
intergenic region is common to only a sub-lineage of 8325-4
strains including SH1000. This deletion was found to
significantly decrease (75\%) steady state sarS but not spa
transcript levels in post-exponential phase. The sub-lineage
8325-4 was also found to harbor 4 additional SNPs. We also found
large sequence variation between 8325, 8325-4 and RN4220 in a
cluster of repetitive hypothetical proteins (SA0282 homologs)
near the Ess secretion cluster. The overall 8325-4 SNP set
results in 17 alterations within coding sequences. Remarkably, we
discovered that all tested strains of the 8325-4 lineage lack
phenol soluble modulin $\alpha$3 (PSM$\alpha$3), a virulence
determinant implicated in neutrophil chemotaxis, biofilm
architecture and surface spreading. Collectively, our results
clarify and define the 8325-4 pedigree and reveal clear evidence
that mutations existing throughout all branches of this lineage,
including the widely used RN6390 and SH1000 strains, could
conceivably impact virulence regulation.",
journal = "PLoS One",
volume = 8,
number = 9,
pages = "e77122",
month = sep,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Matsuo2013-qu,
title = "Comprehensive identification of mutations responsible for
heterogeneous vancomycin-intermediate Staphylococcus aureus
({hVISA)-to-VISA} conversion in laboratory-generated {VISA}
strains derived from {hVISA} clinical strain Mu3",
author = "Matsuo, Miki and Cui, Longzhu and Kim, Jeeyoung and Hiramatsu,
Keiichi",
abstract = "Heterogeneous vancomycin-intermediate Staphylococcus aureus
(hVISA) spontaneously produces VISA cells within its cell
population at a frequency of 10(-6) or greater. We established a
total of 45 VISA mutant strains independently obtained from hVISA
Mu3 and its related strains by one-step vancomycin selection. We
then performed high-throughput whole-genome sequencing of the 45
strains and their parent strains to identify the genes involved
in the hVISA-to-VISA phenotypic conversion. A comparative genome
study showed that all the VISA strains tested carried a unique
set of mutations. All of the 45 VISA strains carried 1 to 4
mutations possibly affecting the expression of a total of 48
genes. Among them, 32 VISA strains carried only one gene affected
by a single mutation. As many as 20 genes in more than eight
functional categories were affected in the 32 VISA strains, which
explained the extremely high rates of the hVISA-to-VISA
phenotypic conversion. Five genes, rpoB, rpoC, walK, pbp4, and
pp2c, were previously reported as being involved in vancomycin
resistance. Fifteen remaining genes were newly identified as
associated with vancomycin resistance in this study. The gene
most frequently affected (6 out of 32 strains) was cmk, which
encodes cytidylate kinase, followed closely by rpoB (5 out of
32), encoding the $\beta$ subunit of RNA polymerase. A mutation
prevalence study also revealed a sizable number of cmk mutants
among clinical VISA strains (7 out of 38 [18\%]). Reduced
cytidylate kinase activity in cmk mutant strains is proposed to
contribute to the hVISA-to-VISA phenotype conversion by
thickening the cell wall and reducing the cell growth rate.",
journal = "Antimicrob. Agents Chemother.",
volume = 57,
number = 12,
pages = "5843--5853",
month = dec,
year = 2013,
keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Chen2013-cu,
title = "Complete genome sequence of a {Pant{\'o}n-Valentine}
leukocidin-negative community-associated methicillin-resistant
Staphylococcus aureus strain of sequence type 72 from Korea",
author = "Chen, Yan and Chatterjee, Som S and Porcella, Stephen F and Yu,
Yun-Song and Otto, Michael",
abstract = "In the past decade, community-associated (CA-) infections with
methicillin-resistant Staphylococcus aureus (MRSA) have emerged
throughout the world. Different CA-MRSA strains dominate in
different geographical locations. Many CA-MRSA lineages contain
genes coding for the Pant{\'o}n-Valentine leukocidin. However,
the role of this leukotoxin in CA-MRSA pathogenesis is still
controversial. The genome sequences of two key PVL-positive
CA-MRSA strains (USA300, USA400) have been reported, but we lack
information on the more recently found PVL-negative CA-MRSA
strains. One such strain is the PVL-negative ST72, the main cause
of CA-MRSA infections in Korea. Here, we report the entire genome
sequence of CA-MRSA ST72 and analyze its gene content with a
focus on virulence factors. Our results show that this strain
does not have considerable differences in virulence factor
content compared to other CA-MRSA strains (USA300, USA400),
indicating that other toxins do not substitute for the lack of
PVL in ST72. This finding is in accordance with the notion that
differential expression of widespread virulence determinants,
rather than the acquisition of additional virulence factors on
mobile genetic elements, such as PVL, is responsible for the
increased virulence of CA- compared to hospital-associated MRSA.",
journal = "PLoS One",
volume = 8,
number = 8,
pages = "e72803",
month = aug,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Yoon2013-gy,
title = "Characterization and genomic analysis of two Staphylococcus
aureus bacteriophages isolated from poultry/livestock farms",
author = "Yoon, Hyunjin and Yun, Jiae and Lim, Jeong-A and Roh, Eunjung and
Jung, Kyu-Seok and Chang, Yoonjee and Ryu, Sangryeol and Heu,
Sunggi",
abstract = "Staphylococcus aureus is one of the most important pathogens,
causing various diseases in humans and animals. As
methicillin-resistant S. aureus (MRSA) has become increasingly
prevalent, controlling this pathogen with standard antibiotic
treatment has become challenging. Bacteriophages (phages) have
attracted interest as alternative antibacterial agents to control
MRSA. In this study, we isolated six S. aureus phages from soils
of poultry/livestock farms. Based on the results of host range
determination with 150 S. aureus strains and restriction enzyme
treatment of phage DNA, two phages, designated SP5 and SP6, were
selected for further characterization and genome sequencing. Both
SP5 and SP6 were classified as members of the family
Siphoviridae. The genome of SP5 comprises 43 305 bp and contains
63 ORFs, while the SP6 genome comprises 42 902 bp and contains 61
ORFs. Although they have different host spectra, the phage
genomes exhibit high nucleotide similarity to each other.
Adsorption assay results suggested that the host range
determinants of the two phages are involved in both adsorption
and infection. Comparative genomic analyses of the two phages
provided evidence that the lysogenic/lytic control module and
tail proteins may be important for host specificity.",
journal = "J. Gen. Virol.",
volume = 94,
number = "Pt 11",
pages = "2569--2576",
month = nov,
year = 2013,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Botelho2016-yb,
title = "Complete genome sequence of an agr-dysfunctional variant of the
{ST239} lineage of the methicillin-resistant Staphylococcus
aureus strain {GV69} from Brazil",
author = "Botelho, Ana M N and Costa, Maiana O C and Beltrame, Cristiana O
and Ferreira, Fabienne A and C{\^o}rtes, Marina F and Bandeira,
Paula T and Lima, Nicholas C B and Souza, Rangel C and Almeida,
Luiz G P and Vasconcelos, Ana T R and Nicol{\'a}s, Marisa F and
Figueiredo, Agnes M S",
abstract = "Staphylococcus aureus is a versatile Gram-positive coccus
frequently found colonizing the skin and nasal membranes of
humans. The acquisition of the staphylococcal cassette chromosome
mec was a major milestone in the evolutionary path of
methicillin-resistant S. aureus. This genetic element carries the
mecA gene, the main determinant of methicillin resistance. MRSA
is involved in a plethora of opportunistic infectious diseases.
The accessory gene regulator is the major S. aureus quorum
sensing system, playing an important role in staphylococcal
virulence, including the development of biofilms. We report the
complete genome sequence (NCBI BioProject ID: PRJNA264181) of the
methicillin-resistant S. aureus strain GV69 (= CMVRS P4521), a
variant of the ST239 lineage that presents with a natural
attenuation of agr-RNAIII transcription and a moderate
accumulation of biofilm.",
journal = "Stand. Genomic Sci.",
volume = 11,
pages = "34",
month = may,
year = 2016,
keywords = "Complete genome sequence; Methicillin-resistant Staphylococcus
aureus; ST239; Skin hospital infection; agr
dysfunction;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Gaviria-Agudelo2015-oi,
title = "Genomic Heterogeneity of Methicillin Resistant Staphylococcus
aureus Associated with Variation in Severity of Illness among
Children with Acute Hematogenous Osteomyelitis",
author = "Gaviria-Agudelo, Claudia and Aroh, Chukwuemika and Tareen,
Naureen and Wakeland, Edward K and Kim, Minsoo and Copley, Lawson
A",
abstract = "INTRODUCTION: The association between severity of illness of
children with osteomyelitis caused by Methicillin-resistant
Staphylococcus aureus (MRSA) and genomic variation of the
causative organism has not been previously investigated. The
purpose of this study is to assess genomic heterogeneity among
MRSA isolates from children with osteomyelitis who have diverse
severity of illness. MATERIALS AND METHODS: Children with
osteomyelitis were prospectively studied between 2010 and 2011.
Severity of illness of the affected children was determined from
clinical and laboratory parameters. MRSA isolates were analyzed
with next generation sequencing (NGS) and optical mapping.
Sequence data was used for multi-locus sequence typing (MLST),
phylogenetic analysis by maximum likelihood (PAML), and
identification of virulence genes and single nucleotide
polymorphisms (SNP) relative to reference strains. RESULTS: The
twelve children studied demonstrated severity of illness scores
ranging from 0 (mild) to 9 (severe). All isolates were USA300, ST
8, SCC mec IVa MRSA by MLST. The isolates differed from reference
strains by 2 insertions (40 Kb each) and 2 deletions (10 and 25
Kb) but had no rearrangements or copy number variations. There
was a higher occurrence of virulence genes among study isolates
when compared to the reference strains (p = 0.0124). There were
an average of 11 nonsynonymous SNPs per strain. PAML demonstrated
heterogeneity of study isolates from each other and from the
reference strains. DISCUSSION: Genomic heterogeneity exists among
MRSA isolates causing osteomyelitis among children in a single
community. These variations may play a role in the pathogenesis
of variation in clinical severity among these children.",
journal = "PLoS One",
volume = 10,
number = 6,
pages = "e0130415",
month = jun,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Aswani2016-td,
title = "Complete Genome Sequence of Staphylococcus aureus {MCRF184}, a
Necrotizing {Fasciitis-Causing} {Methicillin-Sensitive} Sequence
Type 45 Staphylococcus Strain",
author = "Aswani, Vijay and Mau, Bob and Shukla, Sanjay K",
abstract = "We report here the complete genome sequence of a highly virulent
methicillin-sensitive Staphylococcus aureus strain, MCRF184,
belonging to sequence type 45. This staphylococcal strain was
isolated from a surgical biopsy specimen from a patient with
necrotizing fasciitis.",
journal = "Genome Announc.",
volume = 4,
number = 3,
month = may,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Johnston2016-tz,
title = "Genomic Signatures of Experimental Adaptation to Antimicrobial
Peptides in Staphylococcus aureus",
author = "Johnston, Paul R and Dobson, Adam J and Rolff, Jens",
abstract = "The evolution of resistance against antimicrobial peptides has
long been considered unlikely due to their mechanism of action,
yet experimental selection with AMPs results in rapid evolution
of resistance in several species of bacteria. Although numerous
studies have utilized mutant screens to identify loci that
determine AMP susceptibility, there is a dearth of data
concerning the genomic changes which accompany experimental
evolution of AMP resistance. Using genome re-sequencing we
analysed the mutations which arise during experimental evolution
of resistance to the cationic AMPs iseganan, melittin and
pexiganan, as well as to a combination of melittin and pexiganan,
or to the aminoglycoside antibiotic streptomycin. Analysis of 17
independently replicated Staphylococcus aureus selection lines,
including unselected controls, showed that each AMP selected for
mutations at distinct loci. We identify mutations in genes
involved in the synthesis and maintenance of the cell envelope.
This includes genes previously identified from mutant screens for
AMP resistance, and genes involved in the response to AMPs and
cell-wall-active antibiotics. Furthermore, transposon insertion
mutants were used to verify that a number of the identified genes
are directly involved in determining AMP susceptibility. Strains
selected for AMP resistance under controlled experimental
evolution displayed consistent AMP-specific mutations in genes
which determine AMP susceptibility. This suggests that different
routes to evolve resistance are favored within a controlled
genetic background.",
journal = "G3",
month = apr,
year = 2016,
keywords = "Staphylococcus aureus; antimicrobial peptide resistance;
experimental
evolution;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Ugolotti2016-br,
title = "Whole-genome sequencing as standard practice for the analysis of
clonality in outbreaks of meticillin-resistant Staphylococcus
aureus in a paediatric setting",
author = "Ugolotti, E and Larghero, P and Vanni, I and Bandettini, R and
Tripodi, G and Melioli, G and Di Marco, E and Raso, A and
Biassoni, R",
abstract = "Meticillin-resistant Staphylococcus aureus (MRSA) is one of the
leading causes of hospital-associated infections. This study
investigated the potential use of whole-genome sequencing (WGS)
for surveillance purposes by re-examining MRSA strains related to
past outbreaks among hospitalized paediatric patients. WGS data
ameliorated the genotypic profile previously obtained with Sanger
sequencing and pulsed-field gel electrophoresis typing, and
discriminated between strains that were related and unrelated to
the outbreaks. This allowed strain clonality to be defined with a
higher level of resolution than achieved previously. This study
demonstrates the potential of WGS to trace hospital outbreaks,
which may lead to WGS becoming standard practice in outbreak
investigations.",
journal = "J. Hosp. Infect.",
month = apr,
year = 2016,
keywords = "Hospital-associated infections; MRSA; Paediatric hospital
outbreak; Whole-genome
sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Iguchi2016-kk,
title = "Rapid Acquisition of Linezolid Resistance in
{Methicillin-Resistant} Staphylococcus aureus: Role of
Hypermutation and Homologous Recombination",
author = "Iguchi, Shigekazu and Mizutani, Tomonori and Hiramatsu, Keiichi
and Kikuchi, Ken",
abstract = "BACKGROUND: We previously reported the case of a 64-year-old man
with mediastinitis caused by Staphylococcus aureus in which the
infecting bacterium acquired linezolid resistance after only 14
days treatment with linezolid. We therefore investigated relevant
clinical isolates for possible mechanisms of this rapid
acquisition of linezolid resistance. METHODS: Using clinical S.
aureus isolates, we assessed the in vitro mutation rate and
performed stepwise selection for linezolid resistance. To
investigate homologous recombination, sequences were determined
for each of the 23S ribosomal RNA (23S rRNA) loci; analyzed
sequences spanned the entirety of each 23S rRNA gene, including
domain V, as well as the 16S-23S intergenic spacer regions. We
additionally performed next-generation sequencing on clinical
strains to identify single-nucleotide polymorphisms compared to
the N315 genome. RESULTS: Strains isolated from the patient prior
to linezolid exposure (M5-M7) showed higher-level linezolid
resistance than N315, and the pre-exposure strain (M2) exhibited
more rapid acquisition of linezolid resistance than did N315.
However, the mutation rates of these and contemporaneous clinical
isolates were similar to those of N315, and the isolates did not
exhibit any mutations in hypermutation-related genes. Sequences
of the 23S rRNA genes and 16S-23S intergenic spacer regions were
identical among the pre- and post-exposure clinical strains.
Notably, all of the pre-exposure isolates harbored a recQ
missense mutation (Glu69Asp) with respect to N315; such a lesion
may have affected short sequence recombination (facilitating, for
example, recombination among rrn loci). We hypothesize that this
mechanism contributed to rapid acquisition of linezolid
resistance. CONCLUSIONS: Hypermutation and homologous
recombination of the ribosomal RNA genes, including 23S rRNA
genes, appear not to have been sources of the accelerated
acquisition of linezolid resistance observed in our clinical
case. Increased frequency of short sequence recombination may
have resulted from a recQ variant in the infecting organism.",
journal = "PLoS One",
volume = 11,
number = 5,
pages = "e0155512",
month = may,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Ward2016-qy,
title = "Identification of source and sink populations for the emergence
and global spread of the {East-Asia} clone of
community-associated {MRSA}",
author = "Ward, Melissa J and Goncheva, Mariya and Richardson, Emily and
McAdam, Paul R and Raftis, Emma and Kearns, Angela and Daum,
Robert S and David, Michael Z and Lauderdale, Tsai Ling and
Edwards, Giles F and Nimmo, Graeme R and Coombs, Geoffrey W and
Huijsdens, Xander and Woolhouse, Mark E J and Fitzgerald, J Ross",
abstract = "BACKGROUND: Our understanding of the factors influencing the
emergence, dissemination and global distribution of epidemic
clones of bacteria is limited. ST59 is a major epidemic clone of
community-associated MRSA in East Asia, responsible for extensive
morbidity and mortality, but has a much lower prevalence in other
parts of the world. The geographic origin of ST59 and its
international routes of dissemination are unclear and disputed in
the literature. RESULTS: To investigate the origin and spread of
the ST59 clone, we obtained whole genome sequences of isolates
from four continents, sampled over more than a decade, and
carried out a time-scaled phylogeographic analysis. We discover
that two distinct ST59 clades emerged concurrently, in East Asia
and the USA, but underwent clonal expansion at different times.
The East Asia clade was strongly enriched for gene determinants
associated with antibiotic resistance, consistent with regional
differences in antibiotic usage. Both clones spread independently
to Australia and Europe, and we found evidence of the persistence
of multi-drug resistance following export from East Asia. Direct
transfer of strains between Taiwan and the USA was not observed
in either direction, consistent with geographic niche exclusion.
CONCLUSIONS: Our results resolve a longstanding controversy
regarding the origin of the ST59 clone, revealing the major
global source and sink populations and routes for the spread of
multi-drug resistant clones. Additionally, our findings indicate
that diversification of the accessory genome of epidemic clones
partly reflects region-specific patterns of antibiotic usage,
which may influence bacterial fitness after transmission to
different geographic locations.",
journal = "Genome Biol.",
volume = 17,
number = 1,
pages = "160",
month = jul,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Lozano2012-xl,
title = "Expansion of a Plasmid Classification System for {Gram-Positive}
Bacteria and Determination of the Diversity of Plasmids in
Staphylococcus aureus Strains of Human, Animal, and Food Origins",
author = "Lozano, C and Garcia-Migura, L and Aspiroz, C and Zarazaga, M and
Torres, C and Aarestrup, F M",
journal = "Appl. Environ. Microbiol.",
volume = 78,
number = 16,
pages = "5948--5955",
month = aug,
year = 2012,
keywords = "Staphylococcus;plasmid;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Bosi2016-fz,
title = "Comparative genome-scale modelling of Staphylococcus aureus
strains identifies strain-specific metabolic capabilities linked
to pathogenicity",
author = "Bosi, Emanuele and Monk, Jonathan M and Aziz, Ramy K and Fondi,
Marco and Nizet, Victor and Palsson, Bernhard {\O}",
abstract = "Staphylococcus aureus is a preeminent bacterial pathogen capable
of colonizing diverse ecological niches within its human host. We
describe here the pangenome of S. aureus based on analysis of
genome sequences from 64 strains of S. aureus spanning a range of
ecological niches, host types, and antibiotic resistance
profiles. Based on this set, S. aureus is expected to have an
open pangenome composed of 7,411 genes and a core genome composed
of 1,441 genes. Metabolism was highly conserved in this core
genome; however, differences were identified in amino acid and
nucleotide biosynthesis pathways between the strains.
Genome-scale models (GEMs) of metabolism were constructed for the
64 strains of S. aureus These GEMs enabled a systems approach to
characterizing the core metabolic and panmetabolic capabilities
of the S. aureus species. All models were predicted to be
auxotrophic for the vitamins niacin (vitamin B3) and thiamin
(vitamin B1), whereas strain-specific auxotrophies were predicted
for riboflavin (vitamin B2), guanosine, leucine, methionine, and
cysteine, among others. GEMs were used to systematically analyze
growth capabilities in more than 300 different growth-supporting
environments. The results identified metabolic capabilities
linked to pathogenic traits and virulence acquisitions. Such
traits can be used to differentiate strains responsible for mild
vs. severe infections and preference for hosts (e.g., animals vs.
humans). Genome-scale analysis of multiple strains of a species
can thus be used to identify metabolic determinants of virulence
and increase our understanding of why certain strains of this
deadly pathogen have spread rapidly throughout the world.",
journal = "Proc. Natl. Acad. Sci. U. S. A.",
month = jun,
year = 2016,
keywords = "core genome; mathematical modeling; pangenome; pathogenicity;
systems
biology;Staphylococcus;pangenome;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Jaton2016-ll,
title = "Common skin infection due to {Panton-Valentine}
leucocidin-producing Staphylococcus aureus strains in asylum
seekers from Eritrea: a genome-based investigation of a suspected
outbreak",
author = "Jaton, L and Pillonel, T and Jaton, K and Dory, E and Prod'hom, G
and Blanc, D S and Tissot, F and Bodenmann, P and Greub, G",
abstract = "OBJECTIVES: Since late 2014, multiple cases of abscesses and
boils due to methicillin susceptible Staphylococcus aureus (MSSA)
expressing the Panton-Valentine leukocidin (PVL) were observed in
Eritrean asylum seekers in Lausanne, Switzerland. Strains
isolated from infected Eritrean and non-Eritrean patients were
compared by whole genome sequencing (WGS) to determine whether
these numerous cases results from an outbreak. METHODS: The
genome of S. aureus PVL-producing strains were sequenced and
compared. Clinical and epidemiological characteristics of
patients infected by PVL-producing strains were investigated.
RESULTS: This work reports 15 cases of infections due to
PVL-producing strains affecting mostly asylum seekers (n=10),
people working with refugees and/or exposed to Africans (n=3).
Most infections were due to closely related strains of CC152
(n=8) and CC15 (n=3), two distantly related (>34,000 core single
nucleotide polymorphisms [SNPs]) clonal complexes.
Epidemiological link between the 15 cases could be ruled out by
WGS (33 to 172 core SNPs between the different strains of a given
complex). Altogether, these results reflect the probable high
incidence of CC15 and CC152 PVL-producing strains in eastern
Africa. CONCLUSIONS: Clinicians facing unusual skin infections in
African refugees (or in any person returning from this high
endemic region) should consider S. aureus PVL-producer before
suspecting rare infections such as leishmaniosis or
rickettsiosis. Clinicians should also remember that PVL are
frequently expressed by MSSA in some regions of the world and
that antibiotics efficient on the toxin expression, such as
clindamycin, represent the best therapeutic option.",
journal = "Clin. Microbiol. Infect.",
month = jun,
year = 2016,
keywords = "Panton-Valentine leukocidin; ST132; Staphylococcus aureus; genome
sequence; migrants; skin
infection;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Winstel2013-hw,
title = "Wall teichoic acid structure governs horizontal gene transfer
between major bacterial pathogens",
author = "Winstel, Volker and Liang, Chunguang and Sanchez-Carballo,
Patricia and Steglich, Matthias and Munar, Marta and Br{\"o}ker,
Barbara M and Penad{\'e}s, Jose R and N{\"u}bel, Ulrich and
Holst, Otto and Dandekar, Thomas and Peschel, Andreas and Xia,
Guoqing",
abstract = "Mobile genetic elements (MGEs) encoding virulence and resistance
genes are widespread in bacterial pathogens, but it has remained
unclear how they occasionally jump to new host species.
Staphylococcus aureus clones exchange MGEs such as S. aureus
pathogenicity islands (SaPIs) with high frequency via helper
phages. Here we report that the S. aureus ST395 lineage is
refractory to horizontal gene transfer (HGT) with typical S.
aureus but exchanges SaPIs with other species and genera
including Staphylococcus epidermidis and Listeria monocytogenes.
ST395 produces an unusual wall teichoic acid (WTA) resembling
that of its HGT partner species. Notably, distantly related
bacterial species and genera undergo efficient HGT with typical
S. aureus upon ectopic expression of S. aureus WTA. Combined with
genomic analyses, these results indicate that a 'glycocode' of
WTA structures and WTA-binding helper phages permits HGT even
across long phylogenetic distances thereby shaping the evolution
of Gram-positive pathogens.",
journal = "Nat. Commun.",
volume = 4,
pages = "2345",
year = 2013,
keywords = "Staphylococcus;evolution;recombination;phage;Staph\_evolutionary\_history;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Azarian2016-ta,
title = "Intrahost Evolution of {Methicillin-Resistant} Staphylococcus
aureus {USA300} Among Individuals With Reoccurring Skin and
{Soft-Tissue} Infections",
author = "Azarian, Taj and Daum, Robert S and Petty, Lindsay A and
Steinbeck, Jenny L and Yin, Zachary and Nolan, David and
Boyle-Vavra, Susan and Hanage, W P and Salemi, Marco and David,
Michael Z",
abstract = "BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA)
USA300 is the leading cause of MRSA infections in the United
States and has caused an epidemic of skin and soft-tissue
infections. Recurrent infections with USA300 MRSA are common, yet
intrahost evolution during persistence on an individual has not
been studied. This gap hinders the ability to clinically manage
recurrent infections and reconstruct transmission networks.
METHODS: To characterize bacterial intrahost evolution, we
examined the clinical courses of 4 subjects with 3-6 recurrent
USA300 MRSA infections, using patient clinical data, including
antibiotic exposure history, and whole-genome sequencing and
phylogenetic analysis of all available MRSA isolates (n = 29).
RESULTS: Among sequential isolates, we found variability in
diversity, accumulation of mutations, and mobile genetic
elements. Selection for antimicrobial-resistant populations was
observed through both an increase in the number of plasmids
conferring multidrug resistance and strain replacement by a
resistant population. Two of 4 subjects had strain replacement
with a genetically distinct USA300 MRSA population. DISCUSSIONS:
During a 5-year period in 4 subjects, we identified development
of antimicrobial resistance, intrahost evolution, and strain
replacement among isolates from patients with recurrent MRSA
infections. This calls into question the efficacy of
decolonization to prevent recurrent infections and highlights the
adaptive potential of USA300 and the need for effective sampling.",
journal = "J. Infect. Dis.",
volume = 214,
number = 6,
pages = "895--905",
month = sep,
year = 2016,
keywords = "MRSA; Staphylococcus aureus; USA300; antibiotic resistance;
evolution; intrahost; phylogenetic; recurrent infections; skin
and soft-tissue infections; whole-genome sequencing; within
host;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Spoor2015-ub,
title = "Recombination-mediated remodelling of host--pathogen
interactions during Staphylococcus aureus niche adaptation",
author = "Spoor, Laura E and Richardson, Emily and Richards, Amy C and
Wilson, Gillian J and Mendonca, Chriselle and Gupta, Ravi Kr and
McAdam, Paul R and Nutbeam-Tuffs, Stephen and Black, Nikki S and
O'Gara, James P and Lee, Chia Y and Corander, Jukka and Ross
Fitzgerald, J",
abstract = "Large-scale recombination events have led to the emergence of
epidemic clones of several major bacterial pathogens. However,
the functional impact of the recombination on clonal success is
not understood. Here, we identified a novel widespread hybrid
clone (ST71) of livestock-associated Staphylococcus aureus that
evolved from an ancestor belonging to the major bovine lineage
CC97, through multiple large-scale recombination events with
other S. aureus lineages occupying the same ruminant niche. The
recombination events, affecting a 329 kb region of the
chromosome spanning the origin of replication, resulted in
allele replacement and loss or gain of an array of genes
influencing host--pathogen interactions. Of note, molecular
functional analyses revealed that the ST71 hybrid clone has
acquired multiple novel pathogenic traits associated with
acquired and innate immune evasion and bovine extracellular
matrix adherence. These findings provide a paradigm for the
impact of large-scale recombination events on the rapid
evolution of bacterial pathogens within defined ecological
niches.",
journal = "Microbial Genomics",
publisher = "Microbiology Society",
volume = 1,
number = 4,
month = oct,
year = 2015,
keywords = "recombination; remodelling; Staphylococcus aureus;
host--pathogen interactions; niche
adaptation;recombination;Staphylococcus;host-pathogen;Staph\_evolutionary\_history;Staph\_evolutionary\_history/staph
microbial interactions;Staphylococcus\_aureus\_genome\_papers"
}
@UNPUBLISHED{Thorpe2016-nj,
title = "The large majority of intergenic sites in bacteria are
selectively constrained, even when known regulatory elements are
excluded",
author = "Thorpe, Harry A and Bayliss, Sion C and Hurst, Laurence D and
Feil, Edward J",
abstract = "There are currently no broad estimates of the overall strength
and direction of selection operating on intergenic variation in
bacteria. Here we address this using large whole genome sequence
datasets representing six diverse bacterial species; Escherichia
coli, Staphylococcus aureus, Salmonella enterica, Streptococcus
pneumoniae, Klebsiella pneumoniae, and Mycobacterium
tuberculosis. Excluding M. tuberculosis, we find that a high
proportion (62\%-79\%; mean 70\%) of intergenic sites are
selectively constrained, relative to synonymous sites. Non-coding
RNAs tend to be under stronger selective constraint than
promoters, which in turn are typically more constrained than
rho-independent terminators. Even when these regulatory elements
are excluded, the mean proportion of constrained intergenic sites
only falls to 69\%; thus our current understanding of the
functionality of intergenic regions (IGRs) in bacteria is
severely limited. Consistent with a role for positive as well as
negative selection on intergenic sites, we present evidence for
strong positive selection in Mycobacterium tuberculosis
promoters, underlining the key role of regulatory changes as an
adaptive mechanism in this highly monomorphic pathogen.",
journal = "bioRxiv",
pages = "069708",
month = jan,
year = 2016,
keywords = "evolution;Staphylococcus;bacterial comparative
genomics;Staph\_evolutionary\_history/Teaching\_Prokaryotic\_evolution;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;microRNA\_in\_bacteria",
language = "en"
}
@ARTICLE{Santos2016-wg,
title = "Draft Genome Sequence of the Aureocin {A53-Producing} Strain
Staphylococcus aureus {A53}",
author = "Santos, Olinda Cabral Silva and Duarte, Andreza Freitas Souza and
Albano, Rodolpho Mattos and Bastos, Maria Carmo Freire",
abstract = "Here, we present the 2,658,363-bp draft genome sequence of the
aureocin A53-producing strain Staphylococcus aureus A53. This
genome information may contribute to the optimal and rational
exploitation of aureocin A53 as an antimicrobial agent and to its
production in large scale.",
journal = "Genome Announc.",
volume = 4,
number = 4,
month = aug,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Ward2016-pz,
title = "Identification of source and sink populations for the emergence
and global spread of the {East-Asia} clone of
community-associated {MRSA}",
author = "Ward, Melissa J and Goncheva, Mariya and Richardson, Emily and
McAdam, Paul R and Raftis, Emma and Kearns, Angela and Daum,
Robert S and David, Michael Z and Lauderdale, Tsai Ling and
Edwards, Giles F and Nimmo, Graeme R and Coombs, Geoffrey W and
Huijsdens, Xander and Woolhouse, Mark E J and Fitzgerald, J Ross",
abstract = "Our understanding of the factors influencing the emergence,
dissemination and global distribution of epidemic clones of
bacteria is limited. ST59 is a major epidemic clone of
community-associated MRSA in East Asia, responsible for extensive
morbidity and mortality, but has a much lower prevalence in other
parts of the world. The geographic origin of ST59 and its
international routes of dissemination are unclear and disputed in
the literature.",
journal = "Genome Biol.",
volume = 17,
number = 1,
pages = "1--13",
year = 2016,
keywords = "
Staphylococcus;antibiotics;Staph\_evolutionary\_history;bacterial
comparative
genomics;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers;Staph-animal-human"
}
@ARTICLE{Weber2016-fq,
title = "Complete Genome Sequences of Two {Methicillin-Sensitive}
Staphylococcus aureus Isolates Representing a Population Subset
Highly Prevalent in Human Colonization",
author = "Weber, Robert E and Layer, Franziska and Fuchs, Stephan and
Bender, Jennifer K and Fiedler, Stefan and Werner, Guido and
Strommenger, Birgit",
abstract = "Here, we report the high-quality draft genome sequences of two
methicillin-susceptible Staphylococcus aureus isolates, 08-02119
and 08-02300. Belonging to sequence type 582 (ST582) and ST7,
both isolates are representatives of clonal lineages often
associated with asymptomatic colonization of humans.",
journal = "Genome Announc.",
volume = 4,
number = 4,
month = jul,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Senghore2016-mp,
title = "Whole-genome sequencing reveals transmission of Staphylococcus
aureus from humans to green monkeys in The Gambia",
author = "Senghore, Madikay and Bayliss, Sion C and Kwambana-Adams, Brenda
A and Foster-Nyarko, Ebenezer and Manneh, Jainaba and Dione,
Michel and Badji, Henry and Ebruke, Chinelo and Doughty, Emma L
and Thorpe, Harry A and Jasinska, Anna J and Schmitt, Christopher
A and Cramer, Jennifer D and Turner, Trudy R and Weinstock,
George and Freimer, Nelson B and Pallen, Mark J and Feil, Edward
J and Antonio, Martin",
abstract = "Staphylococcus aureus is an important pathogen of humans and
animals. We genome-sequenced ninety S. aureus isolates from the
Gambia: 46 isolates from invasive disease in humans, 13 human
carriage isolates and 31 monkey carriage isolates. We inferred
multiple anthroponotic transmissions of S. aureus from humans to
green monkeys, Chlorocebus sabaeus in The Gambia over different
timescales. We report a novel monkey-associated clade of S.
aureus that emerged from a human-to-monkey switch estimated to
have occurred 2,700 years ago. Adaptation of this lineage to the
monkey host is accompanied by loss of phage-encoded genes that
are known to play an important role in human colonisation. We
also report recent anthroponotic transmission of the
well-characterised human lineages, ST6 and ST15, to monkeys,
probably because of steadily increasing encroachment of humans
into the monkeys' habitat. Although we have found no evidence of
transmission of S. aureus from monkeys to humans, as the two
species come into ever-closer contact there might be an increased
risk of additional inter-species exchanges of potential
pathogens. IMPORTANCE: The population structures of
Staphylococcus aureus in humans and monkeys in sub-Saharan Africa
have been previously described using MLST. However, these data
lack the power to accurately infer details regarding the origin
and maintenance of new adaptive lineages. Here, we describe the
use of whole genome sequencing to detect transmission of S.
aureus between humans and non-human primates and to document the
genetic changes accompanying host adaptation. We note that human
to monkey switches tend to be more common than the reverse, and
that a novel monkey associated clade is likely to have emerged
from such a switch approximately 2700 years ago. Moreover,
analysis of the accessory genome provides important clues as to
the genetic changes underpinning host adaptation, and in
particular show that human to monkey switches tend to be
associated with the loss of genes known to confer adaptation to
the human host.",
journal = "Appl. Environ. Microbiol.",
month = jul,
year = 2016,
keywords = "Staphylococcus;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Monecke2015-ob,
title = "A clonal complex 12 methicillin-resistant Staphylococcus aureus
strain, West Australian {MRSA-59}, harbors a novel
{pseudo-SCCmec} element",
author = "Monecke, Stefan and Coombs, Geoffrey W and Pearson, Julie and
Hotzel, Helmut and Slickers, Peter and Ehricht, Ralf",
abstract = "A West Australian methicillin-resistant Staphylococcus aureus
strain (WA MRSA-59) was characterized by microarray and
sequencing. Its pseudo-staphylococcal cassette chromosome mec
(SCCmec) element comprised dcs, Q9XB68-dcs, mvaS-SCC, Q5HJW6,
dru, ugpQ, ydeM, mecA-mecR-mecI, txbi mecI, tnp IS431, copA2-mco
(copper resistance), ydhK, arsC-arsB-arsR (arsenic resistance),
open reading frame PT43, and per-2. Recombinase genes, xylR
(mecR2), and PSM-mec (phenol-soluble modulin) were absent. We
suggest that mec complex A should be split into two subtypes. One
harbors PSM-mec and xylR (mecR2). It is found in SCCmec types II,
III, and VIII. The second subtype, described herein, is present
in WA MRSA-59 and some coagulase-negative staphylococci.",
journal = "Antimicrob. Agents Chemother.",
volume = 59,
number = 11,
pages = "7142--7144",
month = nov,
year = 2015,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Davis2015-op,
title = "Genome sequencing reveals strain dynamics of
methicillin-resistant Staphylococcus aureus in the same household
in the context of clinical disease in a person and a dog",
author = "Davis, Meghan F and Misic, Ana M and Morris, Daniel O and Moss,
John T and Tolomeo, Pam and Beiting, Daniel P and Nachamkin,
Irving and Lautenbach, Ebbing and Rankin, Shelley C",
abstract = "The strain dynamics of methicillin-resistant Staphylococcus
aureus (MRSA) isolates from people and the household dog were
investigated. The isolates were identified in the context of a
randomized controlled trial that tested household-wide
decolonization of people. Genotypic comparison of MRSA isolates
obtained from two household members, the dog, and home surfaces
over a three-month period failed to implicate the pet or the home
environment in recurrent colonization of the household members.
However, it did implicate the pet's bed in exposure of the dog
prior to the dog's infection. Whole genome sequencing was
performed to differentiate the isolates. This report also
describes introduction of diverse strains of MRSA into the
household within six weeks of cessation of harmonized
decolonization treatment of people and treatment for infection in
the dog. These findings suggest that community sources outside
the home may be important for recurrent MRSA colonization or
infection.",
journal = "Vet. Microbiol.",
volume = 180,
number = "3-4",
pages = "304--307",
month = nov,
year = 2015,
keywords = "Antimicrobial resistance; Canine; MRSA; SSI;
SSTI;Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
}
@ARTICLE{Yan2016-hn,
title = "Genetic features of livestock-associated Staphylococcus aureus
{ST9} isolates from Chinese pigs that carry the lsa(E) gene for
quinupristin/dalfopristin resistance",
author = "Yan, Xiaomei and Li, Zongwei and Chlebowicz, Monika A and Tao,
Xiaoxia and Ni, Ming and Hu, Yuan and Li, Zhen and Grundmann,
Hajo and Murray, Susan and Pascoe, Ben and Sheppard, Samuel K and
Bo, Xiaochen and Dijl, Jan Maarten van and Du, Pengcheng and
Zhang, Minli and You, Yuanhai and Yu, Xiaojie and Meng, Fanliang
and Wang, Shengqi and Zhang, Jianzhong",
abstract = "Whole-genome sequencing (WGS) was used to investigate the genetic
features of the recently identified lsa(E) gene in porcine S.
aureus ST9 isolates. Three quinupristin/dalfopristin-resistant
isolates harboring the lsa(E) gene (two MRSA and one MSSA) were
sequenced. Phylogenetic analysis of 184S. aureus genomes showed
that ST9 porcine isolates belong to a distinct sequence cluster.
Further analysis showed that all isolates were deficient in the
recently described type IV restriction-modification system and
SCCmec type XII was identified in the two MRSA isolates, which
included a rare class C2 mec gene complex. A 24kb $\Psi$SCC
fragment was found in the MRSA and MSSA isolates sharing 99\%
nucleotide sequence homology with the $\Psi$SCCJCSC6690 (O-2)
element of a ST9 MRSA isolate from Thailand (accession number
AB705453). Comparison of these ST9 isolates with 181 publically
available S. aureus genomes identified 24 genes present in all
(100\%) ST9 isolates, that were absent from the most closely
related human isolate. Our analysis suggests that the sequenced
quinupristin/dalfopristin-resistant ST9 lineage represent a
reservoir of mobile genetic elements associated with resistance
and virulence features.",
journal = "Int. J. Med. Microbiol.",
month = aug,
year = 2016,
keywords = "ABC transporters; Livestock-associated;
Quinupristin/dalfopristin; Resistance; ST9; Staphylococcus
aureus;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Hughes2015-sf,
title = "Clonal variation in high- and low-level phenotypic and genotypic
mupirocin resistance of {MRSA} isolates in south-east London",
author = "Hughes, John and Stabler, Richard and Gaunt, Michael and Karadag,
Tacim and Desai, Nergish and Betley, Jason and Ioannou, Avgousta
and Aryee, Anna and Hearn, Pasco and Marbach, Helene and Patel,
Amita and Otter, Jonathan A and Edgeworth, Jonathan D and Tosas
Auguet, Olga",
abstract = "OBJECTIVES: Both low-level mupirocin resistance (LMR) and
high-level mupirocin resistance (HMR) have been identified. The
aim of this study was to determine the epidemiology of LMR and
HMR in MRSA isolates at five hospitals that have used mupirocin
for targeted decolonization as part of successful institutional
control programmes. METHODS: All MRSA identified in three
microbiology laboratories serving five central and south-east
London hospitals and surrounding communities between November
2011 and February 2012 were included. HMR and LMR were determined
by disc diffusion testing. WGS was used to derive multilocus
sequence types (MLSTs) and the presence of HMR and LMR resistance
determinants. RESULTS: Prevalence of either HMR or LMR amongst
first healthcare episode isolates from 795 identified patients
was 9.69\% (95\% CI 7.72-11.96); LMR was 6.29\% (95\% CI
4.70-8.21) and HMR was 3.40\% (95\% CI 2.25-4.90). Mupirocin
resistance was not significantly different in isolates identified
from inpatients at each microbiology laboratory, but was more
common in genotypically defined 'hospital' rather than
'community' isolates (OR 3.17, 95\% CI 1.36-9.30, P = 0.002). LMR
was associated with inpatient stay, previous history of MRSA and
age $\geq$65 years; HMR was associated with age $\geq$65 years
and residential postcode outside London. LMR and HMR varied by
clone, with both being low in the dominant UK MRSA clone ST22
compared with ST8, ST36 and ST239/241 for LMR and with ST8 and
ST36 for HMR. V588F mutation and mupA carriage had high
specificity (>97\%) and area under the curve (>83\%) to
discriminate phenotypic mupirocin resistance, but uncertainty
around the sensitivity point estimate was large (95\% CI
52.50\%-94.44\%). Mutations in or near the mupA gene were found
in eight isolates that carried mupA but were not HMR.
CONCLUSIONS: Mupirocin resistance was identified in <10\% of
patients and varied significantly by clone, implying that changes
in clonal epidemiology may have an important role in determining
the prevalence of resistance in conjunction with selection due to
mupirocin use.",
journal = "J. Antimicrob. Chemother.",
volume = 70,
number = 12,
pages = "3191--3199",
month = dec,
year = 2015,
keywords = "Staphylococcus;antibiotics;confirmed\_SA-resistance-mutation;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Mellmann2016-os,
title = "{Real-Time} Genome Sequencing of Resistant Bacteria Provides
Precision Infection Control in an Institutional Setting",
author = "Mellmann, Alexander and Bletz, Stefan and B{\"o}king, Thomas and
Kipp, Frank and Becker, Karsten and Schultes, Anja and Prior,
Karola and Harmsen, Dag",
abstract = "The increasing prevalence of multidrug-resistant (MDR) bacteria
is a serious global challenge. Here, we studied prospectively
whether bacterial whole-genome sequencing (WGS) for real-time MDR
surveillance is technical feasible, returns actionable results,
and is cost-beneficial. WGS was applied to all MDR isolates of
four species (methicillin-resistant Staphylococcus aureus [MRSA],
vancomycin-resistant Enterococcus faecium, MDR Escherichia coli,
and MDR Pseudomonas aeruginosa) at the University Hospital
Muenster, Muenster, Germany, a tertiary care hospital with 1,450
beds, during two 6-month intervals. Turnaround times (TAT) were
measured, and total costs for sequencing per isolate were
calculated. After cancelling prior policies of preemptive
isolation of patients harboring certain Gram-negative MDR
bacteria in risk areas, the second interval was conducted. During
interval I, 645 bacterial isolates were sequenced. From culture,
TATs ranged from 4.4 to 5.3 days, and costs were €202.49 per
isolate. During interval II, 550 bacterial isolates were
sequenced. Hospital-wide transmission rates of the two most
common species (MRSA and MDR E. coli) were low during interval I
(5.8\% and 2.3\%, respectively) and interval II (4.3\% and 5.0\%,
respectively). Cancellation of isolation of patients infected
with non-pan-resistant MDR E. coli in risk wards did not increase
transmission. Comparing sequencing costs with avoided costs
mostly due to fewer blocked beds during interval II, we saved in
excess of €200,000. Real-time microbial WGS in our institution
was feasible, produced precise actionable results, helped us to
monitor transmission rates that remained low following a
modification in isolation procedures, and ultimately saved costs.",
journal = "J. Clin. Microbiol.",
volume = 54,
number = 12,
pages = "2874--2881",
month = dec,
year = 2016,
keywords = "Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers;Anti-infectives\_course",
language = "en"
}
@ARTICLE{Kleinert2016-mz,
title = "Draft Genome Sequences of Three Northern German Epidemic
Staphylococcus aureus ({ST247}) Strains Containing Multiple
Copies of {IS256}",
author = "Kleinert, Franziska and Kallies, Ren{\'e} and Zweynert, Annegret
and Bierbaum, Gabriele",
abstract = "We report the draft genome sequences of three multiresistant
Staphylococcus aureus strains of sequence type 247 (ST247). The
methicillin-resistant S. aureus (MRSA) SA1450/94 is vancomycin
susceptible, while the clinical MRSA isolate S. aureus SA137/93A
and its spontaneous laboratory mutant SA137/93G are characterized
by intermediate vancomycin susceptibility.",
journal = "Genome Announc.",
volume = 4,
number = 5,
month = sep,
year = 2016,
keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Papers\_for\_Michelle;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers",
language = "en"
}
@ARTICLE{Cao2016-tc,
title = "Identification and functional study of type {III-A} {CRISPR-Cas}
systems in clinical isolates of Staphylococcus aureus",
author = "Cao, Linyan and Gao, Chun-Hui and Zhu, Jiade and Zhao, Liping and
Wu, Qingfa and Li, Min and Sun, Baolin",
abstract = "The CRISPR-Cas (clustered regularly interspaced short palindromic
repeats [CRISPR]-CRISPR associated proteins [Cas]) system can
provide prokaryote with immunity against invading mobile genetic
elements (MGEs) such as phages and plasmids, which are the main
sources of staphylococcal accessory genes. To date, only a few
Staphylococcus aureus strains containing CRISPR-Cas systems have
been identified, but no functional study in these strains has
been reported. In this study, 6 clinical isolates of S. aureus
with type III-A CRISPR-Cas systems were identified, and
whole-genome sequencing and functional study were conducted
subsequently. Genome sequence analysis revealed a close linkage
between the CRISPR-Cas system and the staphylococcal cassette
chromosome mec (SCCmec) element in five strains. Comparative
sequence analysis showed that the type III-A repeats are
conserved within staphylococci, despite of the decreased
conservation in trailer-end repeats. Highly homologous sequences
of some spacers were identified in staphylococcal MGEs, and
partially complementary sequences of spacers were mostly found in
the coding strand of lytic regions in staphylococcal phages.
Transformation experiments showed that S. aureus type III-A
CRISPR-Cas system can specifically prevent plasmid transfer in a
transcription-dependent manner. Base paring between crRNA and
target sequence, the endoribonuclease, and the Csm complex were
proved to be necessary for type III-A CRISPR-Cas immunity.",
journal = "Int. J. Med. Microbiol.",
month = aug,
year = 2016,
keywords = "Prophage; SCCmec; Staphylococcus aureus; Type III-A CRISPR-Cas
system;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Botelho2016-ed,
title = "Complete genome sequence of the {MRSA} isolate {HC1335} from
{ST239} lineage displaying a truncated {AgrC} histidine kinase
receptor",
author = "Botelho, Ana M N and Costa, Maiana O C and Beltrame, Cristiana O
and Ferreira, Fabienne A and Lima, Nicholas C B and Costa, Bruno
S S and de Morais, Guilherme L and Souza, Rangel C and Almeida,
Luiz G P and Vasconcelos, Ana T R and Nicol{\'a}s, Marisa F and
Figueiredo, Agnes M S",
abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) is still one
of the most important hospital pathogen globally. The
multiresistant isolates of the ST239-SCCmecIII lineage are spread
over large geographic regions, colonizing and infecting hospital
patients in virtually all continents. The balance between fitness
(adaptability) and virulence potential is likely to represent an
important issue in the clonal shift dynamics leading the success
of some specific MRSA clones over another. The accessory gene
regulator (agr) is the master quorum sensing system of
staphylococci playing a role in the global regulation of key
virulence factors. Consequently, agr inactivation in S. aureus
may represent a significant mechanism of genetic variability in
the adaptation of this healthcare-associated pathogen. We report
here the complete genome sequence of the methicillin-resistant S.
aureus, isolate HC1335, a variant of the ST239 lineage, which
presents a natural insertion of an IS256 transposase element in
the agrC gene encoding AgrC histidine kinase receptor.",
journal = "Genome Biol. Evol.",
month = sep,
year = 2016,
keywords = "IS256 insertion; ST239 lineage; agrC dysfunction; complete genome
sequence; methicillin-resistant Staphylococcus
aureus;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Harrison2016-eo,
title = "Transmission of methicillin-resistant Staphylococcus aureus in
long-term care facilities and their related healthcare networks",
author = "Harrison, Ewan M and Ludden, Catherine and Brodrick, Hayley J and
Blane, Beth and Brennan, Gr{\'a}inne and Morris, Dearbh{\'a}ile
and Coll, Francesc and Reuter, Sandra and Brown, Nicholas M and
Holmes, Mark A and O'Connell, Brian and Parkhill, Julian and
T{\"o}r{\"o}k, M Estee and Cormican, Martin and Peacock, Sharon J",
abstract = "BACKGROUND: Long-term care facilities (LTCF) are potential
reservoirs for methicillin-resistant Staphylococcus aureus
(MRSA), control of which may reduce MRSA transmission and
infection elsewhere in the healthcare system. Whole-genome
sequencing (WGS) has been used successfully to understand MRSA
epidemiology and transmission in hospitals and has the potential
to identify transmission between these and LTCF. METHODS: Two
prospective observational studies of MRSA carriage were conducted
in LTCF in England and Ireland. MRSA isolates were whole-genome
sequenced and analyzed using established methods. Genomic data
were available for MRSA isolated in the local healthcare systems
(isolates submitted by hospitals and general practitioners).
RESULTS: We sequenced a total of 181 MRSA isolates from the two
study sites. The majority of MRSA were multilocus sequence type
(ST)22. WGS identified one likely transmission event between
residents in the English LTCF and three putative transmission
events in the Irish LTCF. WGS also identified closely related
isolates present in colonized Irish residents and their immediate
environment. Based on phylogenetic reconstruction, closely
related MRSA clades were identified between the LTCF and their
healthcare referral network, together with putative MRSA
acquisition by LTCF residents during hospital admission.
CONCLUSIONS: These data confirm that MRSA is transmitted between
residents of LTCF and is both acquired and transmitted to others
in referral hospitals and beyond. Our data present compelling
evidence for the importance of environmental contamination in
MRSA transmission, reinforcing the importance of environmental
cleaning. The use of WGS in this study highlights the need to
consider infection control in hospitals and community healthcare
facilities as a continuum.",
journal = "Genome Med.",
volume = 8,
number = 1,
pages = "102",
month = oct,
year = 2016,
keywords = "Long-term care facilities; MRSA; Molecular epidemiology; Nursing
home; Staphylococcus aureus; Transmission; Whole-genome
sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Van_Duijkeren2016-pd,
title = "Transmission of {MRSA} between humans and animals on duck and
turkey farms",
author = "van Duijkeren, E and Hengeveld, P and Zomer, T P and Landman, F
and Bosch, T and Haenen, A and van de Giessen, A",
abstract = "OBJECTIVES: The objectives of this study were to estimate the
prevalence of MRSA on duck and turkey farms, identify risk
factors for human carriage and study transmission between animals
and humans. METHODS: On 10 duck and 10 turkey farms, samples were
taken from animals, poultry houses, home residences and humans
and cultured using pre-enrichment and selective enrichment. MRSA
isolates were typed by spa typing and multiple-locus variable
number tandem repeat analysis (MLVA) typing. A subset of isolates
from animals and humans was investigated using whole-genome
mapping. RESULTS: MRSA was found on one duck farm and three
turkey farms. On duck farms, all humans were MRSA negative. On
turkey farms, 5 of 11 farmers, 2 of 32 family members and 15 of
49 samples from the home residences were MRSA positive.
Individuals with daily contact with turkeys were significantly
more often MRSA positive than individuals without daily contact.
All MRSA isolates belonged to livestock-associated MLVA complex
398, belonged to spa type t011, were negative for
Panton-Valentine leucocidin, were mecC negative and were mecA
positive. Whole-genome mapping proved a valuable tool to study
the transmission of livestock-associated MRSA and showed that on
two turkey farms the isolates from the animals and humans were
indistinguishable or closely related, indicating transmission.
CONCLUSIONS: MRSA carriage in individuals in daily contact with
turkeys was significantly higher than that in individuals only
living on the farms or than in the general Dutch population.
Therefore, persons with a high degree of contact with turkeys
have an increased risk of MRSA carriage, and we propose that they
should be screened prior to hospitalization in order to decrease
the risk of nosocomial transmission.",
journal = "J. Antimicrob. Chemother.",
volume = 71,
number = 1,
pages = "58--62",
month = jan,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Suhaili2016-gq,
title = "Draft genome sequence of Staphylococcus aureus {KT/312045}, an
{ST1-MSSA} {PVL} positive isolated from pus sample in East Coast
Malaysia",
author = "Suhaili, Zarizal and Lean, Soo-Sum and Mohamad, Noor Muzamil and
Rachman, Abdul R Abdul and Desa, Mohd Nasir Mohd and Yeo, Chew
Chieng",
abstract = "Most of the efforts in elucidating the molecular relatedness and
epidemiology of Staphylococcus aureus in Malaysia have been
largely focused on methicillin-resistant S. aureus (MRSA).
Therefore, here we report the draft genome sequence of the
methicillin-susceptible Staphylococcus aureus (MSSA) with
sequence type 1 (ST1), spa type t127 with Panton-Valentine
Leukocidin (pvl) pathogenic determinant isolated from pus sample
designated as KT/314250 strain. The size of the draft genome is
2.86 Mbp with 32.7\% of G + C content consisting 2673 coding
sequences. The draft genome sequence has been deposited in
DDBJ/EMBL/GenBank under the accession number AOCP00000000.",
journal = "Genom Data",
volume = 9,
pages = "111--112",
month = sep,
year = 2016,
keywords = "Methicillin-susceptible Staphylococcus aureus; Panton-Valentibe
Leukocidin; ST1-MSSA PVL positive Malaysia
isolates;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Azarian2016-bd,
title = "Genomic Epidemiology of {Methicillin-Resistant} Staphylococcus
aureus in a Neonatal Intensive Care Unit",
author = "Azarian, Taj and Maraqa, Nizar F and Cook, Robert L and Johnson,
Judith A and Bailey, Christine and Wheeler, Sarah and Nolan,
David and Rathore, Mobeen H and Morris, Jr, J Glenn and Salemi,
Marco",
abstract = "Despite infection prevention efforts, neonatal intensive care
unit (NICU) patients remain at risk of Methicillin-resistant
Staphylococcus aureus (MRSA) infection. Modes of transmission for
healthcare-associated (HA) and community-associated (CA) MRSA
remain poorly understood and may vary by genotype, hindering the
development of effective prevention and control strategies. From
2008-2010, all patients admitted to a level III NICU were
screened for MRSA colonization, and all available isolates were
spa-typed. Spa-type t008, the most prevalent CA- genotype in the
United States, spa-type t045, a HA- related genotype, and a
convenience sample of strains isolated from 2003-2011, underwent
whole-genome sequencing and phylodynamic analysis. Patient risk
factors were compared between colonized and noncolonized infants,
and virulence and resistance genes compared between spa-type t008
and non-t008 strains. Epidemiological and genomic data were used
to estimate MRSA importations and acquisitions through
transmission reconstruction. MRSA colonization was identified in
9.1\% (177/1940) of hospitalized infants and associated with low
gestational age and birth weight. Among colonized infants, low
gestational age was more common among those colonized with t008
strains. Our data suggest that approximately 70\% of
colonizations were the result of transmission events within the
NICU, with the remainder likely to reflect importations of
``outside'' strains. While risk of transmission within the NICU
was not affected by spa-type, patterns of acquisition and
importation differed between t008 and t045 strains. Phylodynamic
analysis showed the effective population size of spa-type t008
has been exponentially increasing in both community and hospital,
with spa-type t008 strains possessed virulence genes not found
among t045 strains; t045 strains, in contrast, appeared to be of
more recent origin, with a possible hospital source. Our data
highlight the importance of both intra-NICU transmission and
recurrent introductions in maintenance of MRSA colonization
within the NICU environment, as well as spa-type-specific
differences in epidemiology.",
journal = "PLoS One",
volume = 11,
number = 10,
pages = "e0164397",
month = oct,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Wan2016-jx,
title = "Complete Circular Genome Sequence of Successful {ST8/SCCmecIV}
{Community-Associated} {Methicillin-Resistant} Staphylococcus
aureus ({OC8}) in Russia: {One-Megabase} Genomic Inversion,
{IS256's} Spread, and Evolution of Russia {ST8-IV}",
author = "Wan, Tsai-Wen and Khokhlova, Olga E and Iwao, Yasuhisa and
Higuchi, Wataru and Hung, Wei-Chun and Reva, Ivan V and Singur,
Olga A and Gostev, Vladimir V and Sidorenko, Sergey V and
Peryanova, Olga V and Salmina, Alla B and Reva, Galina V and
Teng, Lee-Jene and Yamamoto, Tatsuo",
abstract = "ST8/SCCmecIV community-associated methicillin-resistant
Staphylococcus aureus (CA-MRSA) has been a common threat, with
large USA300 epidemics in the United States. The global
geographical structure of ST8/SCCmecIV has not yet been fully
elucidated. We herein determined the complete circular genome
sequence of ST8/SCCmecIVc strain OC8 from Siberian Russia. We
found that 36.0\% of the genome was inverted relative to USA300.
Two IS256, oppositely oriented, at IS256-enriched hot spots were
implicated with the one-megabase genomic inversion (MbIN) and
vSa$\beta$ split. The behavior of IS256 was flexible: its
insertion site (att) sequences on the genome and junction
sequences of extrachromosomal circular DNA were all divergent,
albeit with fixed sizes. A similar multi-IS256 system was
detected, even in prevalent ST239 healthcare-associated MRSA in
Russia, suggesting IS256's strong transmission potential and
advantage in evolution. Regarding epidemiology, all ST8/SCCmecIVc
strains from European, Siberian, and Far Eastern Russia, examined
had MbIN, and geographical expansion accompanied divergent spa
types and resistance to fluoroquinolones, chloramphenicol, and
often rifampicin. Russia ST8/SCCmecIVc has been associated with
life-threatening infections such as pneumonia and sepsis in both
community and hospital settings. Regarding virulence, the OC8
genome carried a series of toxin and immune evasion genes, a
truncated giant surface protein gene, and IS256 insertion
adjacent to a pan-regulatory gene. These results suggest that
unique single ST8/spa1(t008)/SCCmecIVc CA-MRSA (clade, Russia
ST8-IVc) emerged in Russia, and this was followed by large
geographical expansion, with MbIN as an epidemiological marker,
and fluoroquinolone resistance, multiple virulence factors, and
possibly a multi-IS256 system as selective advantages.",
journal = "PLoS One",
volume = 11,
number = 10,
pages = "e0164168",
month = oct,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers",
language = "en"
}
@ARTICLE{Bletz2015-ks,
title = "Ensuring backwards compatibility: traditional genotyping efforts
in the era of whole genome sequencing",
author = "Bletz, S and Mellmann, A and Rothg{\"a}nger, J and Harmsen, D",
abstract = "When using next-generation whole genome sequencing (WGS),
extraction of spa types from WGS data is essential for backwards
compatibility with Sanger sequencing-based spa typing of
methicillin-resistant Staphylococcus aureus (MRSA). We evaluated
WGS-based spa typing with a 2$\times$250 bp protocol in a diverse
collection of 423 MRSA isolates using two pipelines that executed
sequence quality-trimming and de novo assembly before spa typing.
The SeqSphere(+) pipeline correctly typed 419 isolates (99.1\%)
whereas the CLCbio pipeline succeeded in 249 isolates (58.9\%).
In summary, WGS combined with an optimized de novo assembly
enables nearly full compatibility with Sanger sequencing-based
spa typing data.",
journal = "Clin. Microbiol. Infect.",
volume = 21,
number = 4,
pages = "347.e1--4",
month = apr,
year = 2015,
keywords = "Backwards compatibility; Staphylococcus aureus;
methicillin-resistant Staphylococcus aureus; spa typing; whole
genome
sequencing;Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Sarrou2016-yj,
title = "Characterization of a Novel lsa(E)- and {lnu(B)-Carrying}
Structure Located in the Chromosome of a Staphylococcus aureus
Sequence Type 398 Strain",
author = "Sarrou, S and Liakopoulos, A and Tsoumani, K and Sagri, E and
Mathiopoulos, K D and Tzouvelekis, L S and Miriagou, V and
Petinaki, E",
journal = "Antimicrob. Agents Chemother.",
volume = 60,
number = 2,
pages = "1164--1166",
month = feb,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Kaur2016-ib,
title = "Genome sequencing, assembly, annotation and analysis of
\textit{Staphylococcus xylosus} strain {DMB3-Bh1} reveals genes
responsible for pathogenicity",
author = "Kaur, Gurwinder and Arora, Amit and Sathyabama, Sathyaseelan and
Mubin, Nida and Verma, Sheenam and Mayilraj, Shanmugam and
Agrewala, Javed N",
abstract = "BACKGROUND: Staphylococcus xylosus is coagulase-negative
staphylococci (CNS), found occasionally on the skin of humans but
recurrently on other mammals. Recent reports suggest that this
commensal bacterium may cause diseases in humans and other
animals. In this study, we present the first report of whole
genome sequencing of S. xylosus strain DMB3-Bh1, which was
isolated from the stool of a mouse. RESULTS: The draft genome of
S. xylosus strain DMB3-Bh1 consisted of 2,81,0255 bp with G+C
content of 32.7 mol\%, 2623 predicted coding sequences (CDSs) and
58 RNAs. The final assembly contained 12 contigs of total size
2,81,0255 bp with N50 contig length of 4,37,962 bp and the
largest contig assembled measured 7,61,338 bp. Further, an
interspecies comparative genomic analysis through rapid
annotation using subsystem technology server was achieved with
Staphylococcus aureus RF122 that revealed 36 genes having
similarity with S. xylosus DMB3-Bh1. 35 genes encoded for
virulence, disease and defense and 1 gene encoded for phages,
prophages and transposable elements. CONCLUSIONS: These results
suggest co linearity in genes between S. xylosus DMB3-Bh1 and S.
aureus RF122 that contribute to pathogenicity and might be the
result of horizontal gene transfer. The study indicates that S.
xylosus DMB3-Bh1 may be a potential emerging pathogen for
rodents.",
journal = "Gut Pathog.",
volume = 8,
pages = "55",
month = nov,
year = 2016,
keywords = "CDSs; Coagulase-negative staphylococci; Disease and defense;
EzTaxon; Rapid annotation using subsystem technology (RAST);
Staphylococcus aureus;
Virulence;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Price2016-vt,
title = "Transmission of Staphylococcus aureus between healthcare
workers, the environment and patients in an intensive care unit:
a whole-genome sequencing based longitudinal cohort study",
author = "Price, J R and Cole, K and Bexley, A and Kostiou, V and Eyre, D
W and Golubchik, T and Wilson, D and Crook, D W and Walker, A S
and Peto, T and Llewelyn, M and Paul, J",
abstract = "UCL Discovery is UCL's open access repository, showcasing and
providing access to UCL research outputs from all UCL
disciplines.",
journal = "Lancet Infect. Dis.",
publisher = "Elsevier",
month = dec,
year = 2016,
keywords = "Staphylococcus;bacterial comparative
genomics;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Singh2016-ge,
title = "In Vitro Tolerance of A {Drug-Na{\"\i}ve} Staphylococcus aureus
{FDA209P} towards Vancomycin",
author = "Singh, Madhuri and Matsuo, Miki and Sasaki, Takashi and Morimoto,
Yuh and Hishinuma, Tomomi and Hiramatsu, Keiichi",
abstract = "The mechanisms underlying bacterial tolerance to antibiotics are
unclear. A possible adaptation strategy has now been explored by
exposure of drug-na{\"\i}ve methicillin-susceptible
Staphylococcus aureus strain FDA209P to vancomycin in vitro
Vancomycin-survivor strains, which appeared after 96 h of
exposure, were slow-growing derivatives of the parent strain.
Although the vancomycin minimum-inhibitory concentrations (MICs)
with the survivor strains were within the susceptible range, the
cytokilling effects of vancomycin at 20-fold MIC were
significantly lower than those in the parent strain. Whole-genome
sequencing demonstrated that ileS, encoding isoleucyl-tRNA
synthetase (IleRS), was mutated in two of the three
vancomycin-survivor strains. The IleRS Y723H mutation is located
close to the isoleucyl-tRNA contact site, and potentially affects
the binding affinity of IleRS for isoleucyl-tRNA, thereby
inhibiting protein synthesis and leading to vancomycin tolerance.
Introduction of the mutation encoding IleRS Y723H into FDA209P by
allelic replacement successfully transferred the
vancomycin-tolerance phenotype. We have identified mutation of
ileS as one of the bona fide genetic events leading to the
acquisition of vancomycin tolerance in S. aureus, potentially
acting via inhibition of the function of IleRS.",
journal = "Antimicrob. Agents Chemother.",
month = nov,
year = 2016,
keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Sharma2016-bu,
title = "{Livestock-Associated} Methicillin Resistant
\textit{Staphylococcus aureus} ({LA-MRSA}) Clonal Complex ({CC})
398 Isolated from {UK} Animals belong to European Lineages",
author = "Sharma, Meenaxi and Nunez-Garcia, Javier and Kearns, Angela M and
Doumith, Michel and Butaye, Patrick R and Argud{\'\i}n, M Angeles
and Lahuerta-Marin, Angela and Pichon, Bruno and AbuOun, Manal
and Rogers, Jon and Ellis, Richard J and Teale, Christopher and
Anjum, Muna F",
abstract = "In recent years, there has been an increase in the number of
livestock-associated methicillin resistant Staphylococcus aureus
(LA-MRSA) clonal complex (CC) 398 recovered from S. aureus
isolated animals in the UK. To determine possible origins of 12
LA-MRSA CC398 isolates collected after screening more than a
thousand S. aureus animal isolates from the UK between 2013 and
2015, whole genome sequences (WGS) of CC398 European, including
UK, and non-European isolates from diverse animal hosts were
compared. Phylogenetic reconstruction applied to WGS data to
assess genetic relatedness of all 89 isolates, clustered the 12
UK CC398 LA-MRSA within the European sub-lineages, although on
different nodes; implicating multiple independent incursions into
the UK, as opposed to a single introduction followed by clonal
expansion. Three UK isolates from healthy pigs and one from
turkey clustered within the cassette chromosome recombinases ccr
C S. aureus protein A (spa)-type t011 European sub-lineage and
three UK isolates from horses within the ccrA2B2 t011 European
sub-lineage. The remaining UK isolates, mostly from pigs,
clustered within the t034 European lineage. Presence of
virulence, antimicrobial (AMR), heavy metal (HMR), and
disinfectant (DR) resistance genes were determined using an
in-house pipeline. Most, including UK isolates, harbored
resistance genes to $\geq$3 antimicrobial classes in addition to
$\beta$-lactams. HMR genes were detected in most European ccrC
positive isolates, with >80\% harboring czrC, encoding zinc and
cadmium resistance; in contrast ~60\% ccrC isolates within
non-European lineages and 6\% ccrA2B2 isolates showed this
characteristic. The UK turkey MRSA isolate did not harbor
$\varphi$AV$\beta$ avian prophage genes (SAAV\_2008 and
SAAV\_2009) present in US MSSA isolates from turkey and pigs.
Absence of some of the major human-associated MRSA toxigenic and
virulence genes in the UK LA-MRSA animal isolates was not
unexpected. Therefore, we can conclude that the 12 UK LA-MRSA
isolates collected in the past 2 years most likely represent
separate incursions into the UK from other European countries.
The presence of zinc and cadmium resistance in all nine food
animal isolates (pig and poultry), which was absent from the 3
horse isolates may suggest heavy metal use/exposure has a
possible role in selection of some MRSA.",
journal = "Front. Microbiol.",
volume = 7,
pages = "1741",
month = nov,
year = 2016,
keywords = "UK CC398s; avian prophage genes; methicillin resistant
Staphylococcus aureus in animals; whole genome sequencing; zinc
and cadmium
resistance;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Meumann2016-kp,
title = "Whole genome sequencing to investigate a putative outbreak of
the virulent community-associated methicillin-resistant
Staphylococcus aureus {ST93} clone in a remote Indigenous
community",
author = "Meumann, Ella M and Andersson, Patiyan and Yeaman, Fiona and
Oldfield, Sarah and Lilliebridge, Rachael and Bentley, Stephen D
and Krause, Vicki and Beaman, Miles and Currie, Bart J and Holt,
Deborah C and Giffard, Philip M and Tong, Steven Y C",
abstract = "We report two cases of severe pneumonia due to ST93 MRSA
presenting from a remote Australian Indigenous community within
a 2-week period, and utilised whole genome sequences to
determine whether these were part of an outbreak. S. aureus was
isolated from 12 of 92 nasal swabs collected from 25 community
households (including the two index households); 1 isolate was
ST93. Three of 5 skin lesion S. aureus isolates obtained at the
community were ST93. Whole genome sequencing of the ST93
isolates from this study and a further 20 ST93 isolates from the
same region suggested that recent transmission and progression
to disease had not taken place. The proximity in time and space
of the 2 severe pneumonia cases is likely a reflection of the
high burden of disease due to ST93 MRSA in this population where
skin infections and household crowding are common.",
journal = "Microbial Genomics",
publisher = "Microbiology Society",
month = nov,
year = 2016,
keywords = "colonization;Staphylococcus;bacterial comparative
genomics;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Sabat2017-po,
title = "Complete-genome sequencing elucidates outbreak dynamics of
{CA-MRSA} {USA300} ({ST8-spa} t008) in an academic hospital of
Paramaribo, Republic of Suriname",
author = "Sabat, Artur J and Hermelijn, Sandra M and Akkerboom, Viktoria
and Juliana, Amadu and Degener, John E and Grundmann, Hajo and
Friedrich, Alexander W",
abstract = "We report the investigation of an outbreak situation of
methicillin-resistant Staphylococcus aureus (MRSA) that occurred
at the Academic Hospital Paramaribo (AZP) in the Republic of
Suriname from April to May 2013. We performed whole genome
sequencing with complete gap closure for chromosomes and plasmids
on all isolates. The outbreak involved 12 patients and 1
healthcare worker/nurse at the AZP. In total 24 isolates were
investigated. spa typing, genome-wide single nucleotide
polymorphism (SNP) analysis, ad hoc whole genome multilocus
sequence typing (wgMLST), stable core genome MLST (cgMLST) and in
silico PFGE were used to determine phylogenetic relatedness and
to identify transmission. Whole-genome sequencing (WGS) showed
that all isolates were members of genomic variants of the North
American USA300 clone. However, WGS revealed a heterogeneous
population structure of USA300 circulating at the AZP. We
observed up to 8 SNPs or up to 5 alleles of difference by wgMLST
when the isolates were recovered from different body sites of the
same patient or if direct transmission between patients was most
likely. This work describes the usefulness of complete genome
sequencing of bacterial chromosomes and plasmids providing an
unprecedented level of detail during outbreak investigations not
being visible by using conventional typing methods.",
journal = "Sci. Rep.",
volume = 7,
pages = "41050",
month = jan,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Highlander2007-ff,
title = "Subtle genetic changes enhance virulence of methicillin resistant
and sensitive Staphylococcus aureus",
author = "Highlander, Sarah K and Hult{\'e}n, Kristina G and Qin, Xiang and
Jiang, Huaiyang and Yerrapragada, Shailaja and Mason, Jr, Edward
O and Shang, Yue and Williams, Tiffany M and Fortunov, R{\'e}gine
M and Liu, Yamei and Igboeli, Okezie and Petrosino, Joseph and
Tirumalai, Madhan and Uzman, Akif and Fox, George E and Cardenas,
Ana Maria and Muzny, Donna M and Hemphill, Lisa and Ding, Yan and
Dugan, Shannon and Blyth, Peter R and Buhay, Christian J and
Dinh, Huyen H and Hawes, Alicia C and Holder, Michael and Kovar,
Christie L and Lee, Sandra L and Liu, Wen and Nazareth, Lynne V
and Wang, Qiaoyan and Zhou, Jianling and Kaplan, Sheldon L and
Weinstock, George M",
abstract = "BACKGROUND: Community acquired (CA) methicillin-resistant
Staphylococcus aureus (MRSA) increasingly causes disease
worldwide. USA300 has emerged as the predominant clone causing
superficial and invasive infections in children and adults in the
USA. Epidemiological studies suggest that USA300 is more virulent
than other CA-MRSA. The genetic determinants that render
virulence and dominance to USA300 remain unclear. RESULTS: We
sequenced the genomes of two pediatric USA300 isolates: one
CA-MRSA and one CA-methicillin susceptible (MSSA), isolated at
Texas Children's Hospital in Houston. DNA sequencing was
performed by Sanger dideoxy whole genome shotgun (WGS) and 454
Life Sciences pyrosequencing strategies. The sequence of the
USA300 MRSA strain was rigorously annotated. In USA300-MRSA 2658
chromosomal open reading frames were predicted and 3.1 and 27
kilobase (kb) plasmids were identified. USA300-MSSA contained a
20 kb plasmid with some homology to the 27 kb plasmid found in
USA300-MRSA. Two regions found in US300-MRSA were absent in
USA300-MSSA. One of these carried the arginine deiminase operon
that appears to have been acquired from S. epidermidis. The
USA300 sequence was aligned with other sequenced S. aureus
genomes and regions unique to USA300 MRSA were identified.
CONCLUSION: USA300-MRSA is highly similar to other MRSA strains
based on whole genome alignments and gene content, indicating
that the differences in pathogenesis are due to subtle changes
rather than to large-scale acquisition of virulence factor genes.
The USA300 Houston isolate differs from another sequenced USA300
strain isolate, derived from a patient in San Francisco, in
plasmid content and a number of sequence polymorphisms. Such
differences will provide new insights into the evolution of
pathogens.",
journal = "BMC Microbiol.",
volume = 7,
pages = "99",
month = nov,
year = 2007,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Galata2016-sq,
title = "Comparing genome versus proteome-based identification of clinical
bacterial isolates",
author = "Galata, Valentina and Backes, Christina and Laczny, C{\'e}dric
Christian and Hemmrich-Stanisak, Georg and Li, Howard and Smoot,
Laura and Posch, Andreas Emanuel and Schmolke, Susanne and
Bischoff, Markus and von M{\"u}ller, Lutz and Plum, Achim and
Franke, Andre and Keller, Andreas",
abstract = "Whole-genome sequencing (WGS) is gaining importance in the
analysis of bacterial cultures derived from patients with
infectious diseases. Existing computational tools for WGS-based
identification have, however, been evaluated on previously
defined data relying thereby unwarily on the available taxonomic
information.Here, we newly sequenced 846 clinical gram-negative
bacterial isolates representing multiple distinct genera and
compared the performance of five tools (CLARK, Kaiju, Kraken,
DIAMOND/MEGAN and TUIT). To establish a faithful 'gold standard',
the expert-driven taxonomy was compared with identifications
based on matrix-assisted laser desorption/ionization
time-of-flight (MALDI-TOF) mass spectrometry (MS) analysis.
Additionally, the tools were also evaluated using a data set of
200 Staphylococcus aureus isolates.CLARK and Kraken (with k =31)
performed best with 626 (100\%) and 193 (99.5\%) correct species
classifications for the gram-negative and S aureus isolates,
respectively. Moreover, CLARK and Kraken demonstrated highest
mean F-measure values (85.5/87.9\% and 94.4/94.7\% for the two
data sets, respectively) in comparison with DIAMOND/MEGAN (71 and
85.3\%), Kaiju (41.8 and 18.9\%) and TUIT (34.5 and 86.5\%).
Finally, CLARK, Kaiju and Kraken outperformed the other tools by
a factor of 30 to 170 fold in terms of runtime.We conclude that
the application of nucleotide-based tools using k-mers-e.g. CLARK
or Kraken-allows for accurate and fast taxonomic characterization
of bacterial isolates from WGS data. Hence, our results suggest
WGS-based genotyping to be a promising alternative to the
MS-based biotyping in clinical settings. Moreover, we suggest
that complementary information should be used for the evaluation
of taxonomic classification tools, as public databases may suffer
from suboptimal annotations.",
journal = "Brief. Bioinform.",
month = dec,
year = 2016,
keywords = "MALDI-TOF MS; bacteria; taxonomy; whole-genome next-generation
sequencing;Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Bakthavatchalam2016-zq,
title = "Novel Observations in 11 Heteroresistant
{Vancomycin-Intermediate} {Methicillin-Resistant} Staphylococcus
aureus Strains from South India",
author = "Bakthavatchalam, Yamuna Devi and Veeraraghavan, Balaji and Peter,
John Victor and Rajinikanth, Janakiraman and Inbanathan, Francis
Yesurajan and Devanga Ragupathi, Naveen Kumar and Rajamani Sekar,
Suresh Kumar",
abstract = "We report here the draft genome sequences of 11 heteroresistant
vancomycin-intermediate Staphylococcus aureus (hVISA) strains
from bloodstream infection. All strains harbor mutations in
vraSR, graSR, walKR, and/or tcaRAB and are often implicated as
the frequently mutated candidate genes in hVISA phenotypes.",
journal = "Genome Announc.",
volume = 4,
number = 6,
month = dec,
year = 2016,
keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Berenger2016-gq,
title = "Draft {Whole-Genome} Sequence of a {Catalase-Negative}
Staphylococcus aureus subsp. aureus (Sequence Type 25) Strain
Isolated from a Patient with Endocarditis and Septic Arthritis",
author = "Berenger, Byron and Chen, Justin and Bernier, Anne-Marie and
Bernard, Kathryn",
abstract = "Staphylococcus aureus strains without catalase activity are rare,
challenging to identify with conventional biochemical methods,
and, despite a supposed decreased pathogenicity, can still cause
disease. The first whole-genome sequence of a catalase-negative
S. aureus isolate causing severe recurrent invasive infection
with two novel missense mutations in the katA gene is reported
here.",
journal = "Genome Announc.",
volume = 4,
number = 6,
month = dec,
year = 2016,
keywords = "Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Peng2016-ga,
title = "{WalK(S221P)}, a naturally occurring mutation, confers vancomycin
resistance in {VISA} strain {XN108}",
author = "Peng, Huagang and Hu, Qiwen and Shang, Weilong and Yuan, Jizhen
and Zhang, Xiaopeng and Liu, Hui and Zheng, Ying and Hu, Zhen and
Yang, Yi and Tan, Li and Li, Shu and Hu, Xiaomei and Li, Ming and
Rao, Xiancai",
abstract = "OBJECTIVES: Vancomycin-intermediate Staphylococcus aureus (VISA)
strains have spread globally. We previously isolated an ST239
VISA (XN108) with a vancomycin MIC of 12 mg/L. The mechanism for
XN108 resistance to vancomycin was investigated in this study.
METHODS: Genome comparison was performed to characterize
mutations that might contribute to the XN108 resistance
phenotype. The novel mutation WalK(S221P) was identified and
investigated using allelic replacement experiments. Vancomycin
susceptibilities, autolytic activities and morphologies of the
strains were examined. Autophosphorylation activities of WalK and
the WalK(S221P) mutant were determined in vitro with
[$\lambda$-(32)P]ATP, and binding activity of
WalK(S221P)-activated WalR to the promoter region of its target
gene lytM was determined by electrophoretic mobility shift assay.
RESULTS: Genome comparison revealed three mutations, GraS(T136I),
RpoB(H481N) and WalK(S221P), which might be responsible for
vancomycin resistance in XN108. The introduction of WalK(S221P)
to the vancomycin-susceptible strain N315 increased its
vancomycin MIC from 1.5 to 8 mg/L, whereas the allelic
replacement of WalK(S221P) with the native N315 WalK allele in
XN108 decreased its vancomycin MIC from 12 to 4 mg/L. The VISA
strains have thickened cell walls and decreased autolysis,
consistent with observed changes in the expression of genes
involved in cell wall metabolism and virulence regulation.
WalK(S221P) exhibited reduced autophosphorylation, which may lead
to reduced phosphorylation of WalR. WalK(S221P)-phosphorylated
WalR also exhibited a reduced capacity to bind to the lytM
promoter. CONCLUSIONS: The naturally occurring WalK(S221P)
mutation plays a key role in vancomycin resistance in XN108.",
journal = "J. Antimicrob. Chemother.",
month = dec,
year = 2016,
keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Mellmann2017-go,
title = "High Interlaboratory Reproducibility and Accuracy of
{Next-Generation} {Sequencing-Based} Bacterial Genotyping in a
{Ring-Trial}",
author = "Mellmann, Alexander and Andersen, Paal Skytt and Bletz, Stefan
and Friedrich, Alexander W and Kohl, Thomas A and Lilje, Berit
and Niemann, Stefan and Prior, Karola and Rossen, John W and
Harmsen, Dag",
abstract = "Today, next-generation whole genome sequencing (WGS) technology
is increasingly used to determine the genetic relationship of
bacteria on a nearly whole genome level for infection control
purposes and molecular surveillance. Here, we conducted a
multicenter ring-trial comprising five laboratories to determine
the reproducibility and accuracy of WGS-based typing.The
participating laboratories sequenced 20 blind-coded
Staphylococcus aureus DNA samples using the 250 bp paired-end
chemistry for library preparation in a single sequencing run on
an Illumina Miseq sequencer. Run acceptance criteria were
sequencing outputs > 5.6 Gb and Q30 read quality scores > 75\%.
Subsequently, spa typing, multilocus sequence typing (MLST),
ribosomal MLST, and core genome (cg)MLST were performed by the
participants. Moreover, cgMLST target sequence discrepancies in
comparison to the also included and published sequence of quality
control strain ATCC25923 were resolved using Sanger
sequencing.All five laboratories fulfilled the run acceptance
criteria in a single sequencing run without any repetition. Of
the in total 400 possible typing results, 394 reported spa types,
sequence types (ST), rSTs, and cgMLST cluster types were correct
and identical among all laboratories; only six typing results
were missing. Analysis of cgMLST allelic profiles corroborated
this high reproducibility: only 3 (0.0016\%) of in total 183,927
cgMLST allele calls were wrong. Sanger sequencing confirmed all
the 12 discrepancies of the ring-trial results in comparison to
the published sequence of ATCC25923.In summary, this ring-trial
demonstrated the high reproducibility and accuracy of current
NGS-based bacterial typings for molecular surveillance when done
with nearly completely locked down methods.",
journal = "J. Clin. Microbiol.",
month = jan,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Kawada-Matsuo2016-tq,
title = "{C55} bacteriocin produced by {ETB-plasmid} positive
Staphylococcus aureus strains is a key factor for competition
with S. aureus strains",
author = "Kawada-Matsuo, Miki and Shammi, Fariha and Oogai, Yuichi and
Nakamura, Norifumi and Sugai, Motoyuki and Komatsuzawa, Hitoshi",
abstract = "Exfoliative toxin (ET) produced by Staphylococcus aureus is
closely associated with the onset of bullous impetigo. To date,
three ETs (ETA, ETB and ETD) have been identified. The gene
encoding ETB is located in a plasmid designated pETB. Bacteriocin
synthesis genes are also located in this plasmid and
pETB-positive strains reportedly produce the C55 bacteriocin. In
this study, the antibacterial activity against S. aureus strains
of the bacteriocin produced by the pETB-positive strain TY4 was
investigated. This bacteriocin demonstrated antibacterial
activity against all pETB-negative but not pETB-positive strains,
including TY4. Additionally, a TY4- strain from which the pETB
plasmid had been deleted exhibited susceptibility to the
bacteriocin. Further experiments revealed that two immunity
factors (orf 46-47 and orf 48) downstream of the bacteriocin
synthesis genes in the pETB plasmid are associated with immunity
against the bacteriocin produced by TY4. The TY4- with orf46-47
strain exhibited complete resistance to bacteriocin, whereas the
TY4- with orf48 strain exhibited partial resistance. Whether
bacteriocin affects the proportion of each strain when
co-cultured with S. aureus strains was also investigated. When
TY4 or TY4- was co-cultured with 209P strain, which is
susceptible to the bacteriocin, the proportion of 209P
co-cultured with TY4 was significantly less than when 209P was
co-cultured with TY4-, whereas the proportion of TY4- with
orf46-48 co-cultured with TY4 was greater than with TY4-. These
results suggest that the C55 bacteriocin produced by
pETB-positive strains affects the proportion of each strain when
pETB-positive and -negative strains co-exist.",
journal = "Microbiol. Immunol.",
volume = 60,
number = 3,
pages = "139--147",
month = mar,
year = 2016,
keywords = "Staphylococcus aureus; bacteriocin; lantibiotics; two-component
system;Staphylococcus;Staph\_evolutionary\_history;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Stevens2017-ei,
title = "Draft Genome Sequence of Staphylococcus aureus 1608, a Strain
That Caused Toxic Mastitis in Twin Cows",
author = "Stevens, Marc J A and Stephan, Roger and Johler, Sophia",
abstract = "Staphylococcus aureus 1608 is a strain that caused a lethal
mastitis in cows. Here, the draft genome sequence of the strain
is presented.",
journal = "Genome Announc.",
volume = 5,
number = 1,
month = jan,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Milheirico2017-lu,
title = "{MRSA} strains carrying the novel mecC gene: full genome
sequencing identifies in the genetic background several
determinants that modulate the resistant phenotype",
author = "Milheiri{\c c}o, Catarina and de Lencastre, Herm{\'\i}nia and
Tomasz, Alexander",
abstract = "Most MRSA strains are resistant to beta-lactam antibiotics due to
the presence of the mecA gene encoding an extra
penicillin-binding protein (PBP2A) that has low affinity to
virtually all beta-lactam antibiotics. Recently, a new resistance
determinant - the mecC gene - was identified in S. aureus
isolates recovered from humans and dairy cattle. Although having
typically low MICs to beta-lactam antibiotics, MRSA strains with
the mecC determinant are also capable of expressing high levels
of oxacillin resistance when in an optimal genetic background. In
order to test the impact of extensive beta-lactam selection on
the emergence of mecC carrying strains with high levels of
antibiotic resistance, we exposed the prototype mecC MRSA strain
LGA251 to increasing concentrations of oxacillin. LGA251 was able
to rapidly adapt to high concentrations of oxacillin in the
growth medium. In such laboratory mutants with increased levels
of oxacillin resistance, we identified mutations in genes with no
relationship to the mecC regulatory system indicating that the
genetic background plays an important role in the establishment
of the levels of oxacillin resistance. Our data also indicate
that the stringent stress response plays a critical role in the
beta-lactam antibiotic resistant phenotype of MRSA strains
carrying the mecC determinant.",
journal = "Antimicrob. Agents Chemother.",
month = jan,
year = 2017,
keywords = "oxacillin;Staphylococcus;antibiotics;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Kennedy2010-fe,
title = "Complete nucleotide sequence analysis of plasmids in strains of
Staphylococcus aureus clone {USA300} reveals a high level of
identity among isolates with closely related core genome
sequences",
author = "Kennedy, Adam D and Porcella, Stephen F and Martens, Craig and
Whitney, Adeline R and Braughton, Kevin R and Chen, Liang and
Craig, Carly T and Tenover, Fred C and Kreiswirth, Barry N and
Musser, James M and DeLeo, Frank R",
abstract = "A community-associated methicillin-resistant Staphylococcus
aureus (CA-MRSA) strain known as pulsed-field type USA300
(USA300) is epidemic in the United States. Previous comparative
whole-genome sequencing studies demonstrated that there has been
recent clonal emergence of a subset of USA300 isolates, which
comprise the epidemic clone. Although the core genomes of these
isolates are closely related, the level of diversity among USA300
plasmids was not resolved. Inasmuch as these plasmids might
contribute to significant gene diversity among otherwise closely
related USA300 isolates, we performed de novo sequencing of
endogenous plasmids from 10 previously characterized USA300
clinical isolates obtained from different geographic locations in
the United States. All isolates tested contained small (2- to
3-kb) and/or large (27- to 30-kb) plasmids. The large plasmids
encoded heavy metal and/or antimicrobial resistance elements,
including those that confer resistance to cadmium, bacitracin,
macrolides, penicillin, kanamycin, and streptothricin, although
all isolates were sensitive to minocycline, doxycycline,
trimethoprim-sulfamethoxazole, vancomycin, teicoplanin, and
linezolid. One of the USA300 isolates contained an archaic
plasmid that encoded staphylococcal enterotoxins R, J, and P.
Notably, the large plasmids (27 to 28 kb) from 8 USA300
isolates--those that comprise the epidemic USA300 clone--were
virtually identical (99\% identity) and similar to a large
plasmid from strain USA300\_TCH1516 (a previously sequenced
USA300 strain from Houston, TX). These plasmids are largely
divergent from the 37-kb plasmid of FPR3757, the first sequenced
USA300 strain. The high level of plasmid sequence identity among
the majority of closely related USA300 isolates is consistent
with the recent clonal emergence hypothesis for USA300.",
journal = "J. Clin. Microbiol.",
volume = 48,
number = 12,
pages = "4504--4511",
month = dec,
year = 2010,
keywords = "plasmid;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Lima2017-ib,
title = "Genomic information on multidrug-resistant livestock-associated
methicillin-resistant Staphylococcus aureus {ST398} isolated from
a Brazilian patient with cystic fibrosis",
author = "Lima, Danielle F and Cohen, Renata Wf and Rocha, G{\'e}ssica A
and Albano, Rodolpho M and Marques, Elizabeth A and Le{\~a}o,
Robson S",
abstract = "Alarmingly, the isolation of methicillin-resistant Staphylococcus
aureus (MRSA) has been increasing among patients with cystic
fibrosis (CF). During a previous molecular characterisation of
MRSA isolates obtained from patients with CF from Rio de Janeiro,
Brazil, one isolate was identified as the ST398 clone, a
livestock-associated (LA) MRSA. In this study, we report the
draft genome sequence of an LA-MRSA ST398 clone isolated from a
patient with CF.",
journal = "Mem. Inst. Oswaldo Cruz",
volume = 112,
number = 1,
pages = "79--80",
month = jan,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Vestergaard2016-vt,
title = "{Genome-Wide} Identification of Antimicrobial Intrinsic
Resistance Determinants in \textit{Staphylococcus aureus}",
author = "Vestergaard, Martin and Leng, Bingfeng and Haaber, Jakob and
Bojer, Martin S and Vegge, Christina S and Ingmer, Hanne",
abstract = "The emergence of antimicrobial resistance severely threatens our
ability to treat bacterial infections. While acquired resistance
has received considerable attention, relatively little is known
of intrinsic resistance that allows bacteria to naturally
withstand antimicrobials. Gene products that confer intrinsic
resistance to antimicrobial agents may be explored for
alternative antimicrobial therapies, by potentiating the efficacy
of existing antimicrobials. In this study, we identified the
intrinsic resistome to a broad spectrum of antimicrobials in the
human pathogen, Staphylococcus aureus. We screened the Nebraska
Transposon Mutant Library of 1920 single-gene inactivations in S.
aureus strain JE2, for increased susceptibility to the
anti-staphylococcal antimicrobials (ciprofloxacin, oxacillin,
linezolid, fosfomycin, daptomycin, mupirocin, vancomycin, and
gentamicin). Sixty-eight mutants were confirmed by E-test to
display at least twofold increased susceptibility to one or more
antimicrobial agents. The majority of the identified genes have
not previously been associated with antimicrobial susceptibility
in S. aureus. For example, inactivation of genes encoding for
subunits of the ATP synthase, atpA, atpB, atpG and atpH, reduced
the minimum inhibitory concentration (MIC) of gentamicin 16-fold.
To elucidate the potential of the screen, we examined treatment
efficacy in the Galleria mellonella infection model. Gentamicin
efficacy was significantly improved, when treating larvae
infected with the atpA mutant compared to wild type cells with
gentamicin at a clinically relevant concentration. Our results
demonstrate that many gene products contribute to the intrinsic
antimicrobial resistance of S. aureus. Knowledge of these
intrinsic resistance determinants provides alternative targets
for compounds that may potentiate the efficacy of existing
antimicrobial agents against this important pathogen.",
journal = "Front. Microbiol.",
volume = 7,
pages = "2018",
month = dec,
year = 2016,
keywords = "Galleria mellonella; Staphylococcus aureus; antimicrobial agents;
intrinsic resistance; potentiator
targets;Staphylococcus;antibiotics;confirmed\_SA-resistance-mutation;oxacillin;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers",
language = "en"
}
@ARTICLE{Capra2017-co,
title = "Genomic and transcriptomic comparison between Staphylococcus
aureus strains associated with high and low within herd
prevalence of intra-mammary infection",
author = "Capra, E and Cremonesi, P and Pietrelli, A and Puccio, S and
Luini, M and Stella, A and Castiglioni, B",
abstract = "BACKGROUND: Staphylococcus aureus (Staph. aureus) is one of the
major pathogens causing mastitis in dairy ruminants worldwide.
The chronic nature of Staph. aureus infection enhances the
contagiousness risk and diffusion in herds. In order to identify
the factors involved in intra-mammary infection (IMI) and
diffusion in dairy cows, we investigated the molecular
characteristics of two groups of Staph. aureus strains belonging
to ST8 and ST398, differing in clinical properties, through
comparison of whole genome and whole transcriptome sequencing.
RESULTS: The two groups of strains, one originated from high IMI
prevalence herds and the other from low IMI prevalence herds,
present a peculiar set of genes and polymorphisms related to
phenotypic features, such as bacterial invasion of mammary
epithelial cells and host adaptation. Transcriptomic analysis
supports the high propensity of ST8 strain to chronicity of
infection and to a higher potential cytotoxicity. CONCLUSIONS:
Our data are consistent with the invasiveness and host adaptation
feature for the strains GTB/ST8 associated to high within-herd
prevalence of mastitis. Variation in genes coding for surface
exposed proteins and those associated to virulence and defence
could constitute good targets for further research.",
journal = "BMC Microbiol.",
volume = 17,
number = 1,
pages = "21",
month = jan,
year = 2017,
keywords = "Genome; Mastitis; Next generation sequencing; Staphylococcus
aureus; Transcriptome;
Virulence;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Ledda2017-eh,
title = "Re-emergence of methicillin susceptibility in a resistant lineage
of Staphylococcus aureus",
author = "Ledda, Alice and Price, James R and Cole, Kevin and Llewelyn,
Martin J and Kearns, Angela M and Crook, Derrick W and Paul, John
and Didelot, Xavier",
abstract = "OBJECTIVES: MRSA is a leading cause of hospital-associated
infection. Acquired resistance is encoded by the mecA gene or its
homologue mecC, but little is known about the evolutionary
dynamics involved in gain and loss of resistance. The objective
of this study was to obtain an expanded understanding of
Staphylococcus aureus methicillin resistance microevolution in
vivo, by focusing on a single lineage. METHODS: We compared the
whole-genome sequences of 231 isolates from a single epidemic
lineage [clonal complex 30 (CC30) and spa-type t018] of S. aureus
that caused an epidemic in the UK. RESULTS: We show that
resistance to methicillin in this single lineage was gained on at
least two separate occasions, one of which led to a clonal
expansion around 1995 presumably caused by a selective advantage.
Resistance was, however, subsequently lost in vivo by nine
strains isolated between 2008 and 2012. We describe the genetic
mechanisms involved in this loss of resistance and the imperfect
relationship between genotypic and phenotypic resistance.
CONCLUSIONS: The recent re-emergence of methicillin
susceptibility in this epidemic lineage suggests a significant
fitness cost of resistance and reduced selective advantage
following the introduction in the mid-2000s of MRSA hospital
control measures throughout the UK.",
journal = "J. Antimicrob. Chemother.",
month = jan,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Uhlemann2017-db,
title = "Evolutionary Dynamics of Pandemic {Methicillin-Sensitive}
Staphylococcus aureus {ST398} and Its International Spread via
Routes of Human Migration",
author = "Uhlemann, Anne-Catrin and McAdam, Paul R and Sullivan, Sean B and
Knox, Justin R and Khiabanian, Hossein and Rabadan, Raul and
Davies, Peter R and Fitzgerald, J Ross and Lowy, Franklin D",
abstract = "Methicillin-susceptible Staphylococcus aureus (MSSA) accounts for
the majority of S. aureus infections globally, and yet
surprisingly little is known about its clonal evolution. We
applied comparative whole-genome sequencing (WGS) analyses to
epidemiologically and geographically diverse ST398-MSSA, a
pandemic lineage affecting both humans and livestock. Bayesian
phylogenetic analysis predicted divergence of human-associated
ST398-MSSA ~40 years ago. Isolates from Midwestern pigs and
veterinarians differed substantially from those in New York City
(NYC). Pig ST398 strains contained a large region of
recombination representing imports from multiple sequence types
(STs). Phylogeographic analyses supported the spread of
ST398-MSSA along local cultural and migratory links between parts
of the Caribbean, North America, and France, respectively.
Applying pairwise single-nucleotide polymorphism (SNP) distances
as a measure of genetic relatedness between isolates, we observed
that ST398 not only clustered in households but also frequently
extended across local social networks. Isolates collected from
environmental surfaces reflected the full diversity of colonizing
individuals, highlighting their potentially critical role as
reservoirs for transmission and diversification. Strikingly, we
observed high within-host SNP variability compared to our
previous studies on the dominant methicillin-resistant
Staphylococcus aureus (MRSA) clone USA300. Our data indicate that
the dynamics of colonization, persistence, and transmission
differ substantially between USA300-MRSA and ST398-MSSA. Taken
together, our study reveals local and international routes of
transmission for a major MSSA clone, indicating key impacts of
recombination and mutation on genetic diversification and
highlighting important ecological differences from epidemic
USA300. Our study demonstrates extensive local and international
routes of transmission for a major MSSA clone despite the lack of
substantial antibiotic resistance. IMPORTANCE: Unlike
methicillin-resistant Staphylococcus aureus (MRSA), surprisingly
little is known about the clonal evolution of
methicillin-susceptible S. aureus (MSSA), although these strains
account for the majority of S. aureus infections. To better
understand how MSSA spreads and becomes established in
communities, we applied comparative bacterial whole-genome
sequencing to pandemic ST398-MSSA, a clone of clinical importance
affecting humans and livestock in different geographic regions.
Phylogeographic analyses identified that ST398-MSSA spread along
local cultural and migratory links between parts of the
Caribbean, North America, and France, respectively. We observed
high within-host SNP variability compared to our previous studies
on the dominant MRSA clone USA300. Our data indicate that the
dynamics of colonization, persistence, and transmission differ
substantially between USA300 MRSA and ST398 MSSA.",
journal = "MBio",
volume = 8,
number = 1,
month = jan,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Escobar-Perez2017-wu,
title = "Emergence and spread of a new community-genotype
methicillin-resistant Staphylococcus aureus clone in Colombia",
author = "Escobar-Perez, Javier and Reyes, Niradiz and Marquez-Ortiz,
Ricaurte Alejandro and Rebollo, Juan and Pinz{\'o}n, Hernando and
Tovar, Catalina and Moreno-Casta{\~n}eda, Jaime and Corredor,
Zayda Lorena and Castro, Betsy Esperanza and Moncada, Maria
Victoria and Vanegas, Natasha",
abstract = "BACKGROUND: Community-genotype methicillin-resistant
Staphylococcus aureus (CG-MRSA) clones are a global concern due
to their resistance and increased virulence and their ability to
cause infections both hospitalized patients and healthy people in
the community. Here, we characterize 32 isolates of a new CG-MRSA
clone. These isolates were identified in four cities in Colombia,
South America. METHODS: The isolates were recovered from four
different epidemiological and prospective studies that were
conducted in several regions of Colombia. Molecular
characterizations included multilocus sequence typing;
pulsed-field gel electrophoresis; SCCmec, agr and spa typing; and
whole-genome sequencing. RESULTS: All isolates belonged to ST923
(clonal complex 8), harbouring SCCmec IVa and a spa type t1635
and lacking an arginine catabolism mobile element. The isolates
were classified as COL923, were resistant to at least one
non-beta-lactam antibiotic, and exhibited high frequencies
(>60\%) of resistance to macrolides and tetracycline. Using
whole-genome sequencing, we found that this new clone harbours
novel prophage 3 and beta-island structures and a slightly
different pathogenicity island 5. Moreover, isolates belonging to
the COL923 clone are grouped in a different clade than USA300 and
USA300-LV. CONCLUSION: Our results show the emergence and spread
of the COL923 clone in different cities in Colombia. This clone
is resistant to several antibiotics and possesses new structures
in its mobile genetic elements.",
journal = "BMC Infect. Dis.",
volume = 17,
number = 1,
pages = "108",
month = jan,
year = 2017,
keywords = "Colombia; Community; Methicillin-resistant Staphylococcus aureus;
New clone;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Eyre2012-xf,
title = "A pilot study of rapid benchtop sequencing of Staphylococcus
aureus and Clostridium difficile for outbreak detection and
surveillance",
author = "Eyre, David W and Golubchik, Tanya and Gordon, N Claire and
Bowden, Rory and Piazza, Paolo and Batty, Elizabeth M and Ip,
Camilla L C and Wilson, Daniel J and Didelot, Xavier and
O'Connor, Lily and Lay, Rochelle and Buck, David and Kearns,
Angela M and Shaw, Angela and Paul, John and Wilcox, Mark H and
Donnelly, Peter J and Peto, Tim E A and Walker, A Sarah and
Crook, Derrick W",
abstract = "OBJECTIVES: To investigate the prospects of newly available
benchtop sequencers to provide rapid whole-genome data in routine
clinical practice. Next-generation sequencing has the potential
to resolve uncertainties surrounding the route and timing of
person-to-person transmission of healthcare-associated infection,
which has been a major impediment to optimal management. DESIGN:
The authors used Illumina MiSeq benchtop sequencing to undertake
case studies investigating potential outbreaks of
methicillin-resistant Staphylococcus aureus (MRSA) and
Clostridium difficile. SETTING: Isolates were obtained from
potential outbreaks associated with three UK hospitals.
PARTICIPANTS: Isolates were sequenced from a cluster of eight
MRSA carriers and an associated bacteraemia case in an intensive
care unit, another MRSA cluster of six cases and two clusters of
C difficile. Additionally, all C difficile isolates from cases
over 6 weeks in a single hospital were rapidly sequenced and
compared with local strain sequences obtained in the preceding 3
years. MAIN OUTCOME MEASURE: Whole-genome genetic relatedness of
the isolates within each epidemiological cluster. RESULTS:
Twenty-six MRSA and 15 C difficile isolates were successfully
sequenced and analysed within 5 days of culture. Both MRSA
clusters were identified as outbreaks, with most sequences in
each cluster indistinguishable and all within three single
nucleotide variants (SNVs). Epidemiologically unrelated isolates
of the same spa-type were genetically distinct ($\geq$21 SNVs).
In both C difficile clusters, closely epidemiologically linked
cases (in one case sharing the same strain type) were shown to be
genetically distinct ($\geq$144 SNVs). A reconstruction applying
rapid sequencing in C difficile surveillance provided early
outbreak detection and identified previously undetected probable
community transmission. CONCLUSIONS: This benchtop sequencing
technology is widely generalisable to human bacterial pathogens.
The findings provide several good examples of how rapid and
precise sequencing could transform identification of transmission
of healthcare-associated infection and therefore improve hospital
infection control and patient outcomes in routine clinical
practice.",
journal = "BMJ Open",
volume = 2,
number = 3,
month = jun,
year = 2012,
keywords = "Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Harrison2014-mh,
title = "A shared population of epidemic methicillin-resistant
Staphylococcus aureus 15 circulates in humans and companion
animals",
author = "Harrison, Ewan M and Weinert, Lucy A and Holden, Matthew T G and
Welch, John J and Wilson, Katherine and Morgan, Fiona J E and
Harris, Simon R and Loeffler, Anette and Boag, Amanda K and
Peacock, Sharon J and Paterson, Gavin K and Waller, Andrew S and
Parkhill, Julian and Holmes, Mark A",
abstract = "UNLABELLED: Methicillin-resistant Staphylococcus aureus (MRSA) is
a global human health problem causing infections in both
hospitals and the community. Companion animals, such as cats,
dogs, and horses, are also frequently colonized by MRSA and can
become infected. We sequenced the genomes of 46 multilocus
sequence type (ST) 22 MRSA isolates from cats and dogs in the
United Kingdom and compared these to an extensive population
framework of human isolates from the same lineage. Phylogenomic
analyses showed that all companion animal isolates were
interspersed throughout the epidemic MRSA-15 (EMRSA-15) pandemic
clade and clustered with human isolates from the United Kingdom,
with human isolates basal to those from companion animals,
suggesting a human source for isolates infecting companion
animals. A number of isolates from the same veterinary hospital
clustered together, suggesting that as in human hospitals,
EMRSA-15 isolates are readily transmitted in the veterinary
hospital setting. Genome-wide association analysis did not
identify any host-specific single nucleotide polymorphisms (SNPs)
or virulence factors. However, isolates from companion animals
were significantly less likely to harbor a plasmid encoding
erythromycin resistance. When this plasmid was present in
animal-associated isolates, it was more likely to contain
mutations mediating resistance to clindamycin. This finding is
consistent with the low levels of erythromycin and high levels of
clindamycin used in veterinary medicine in the United Kingdom.
This study furthers the ``one health'' view of infectious
diseases that the pathogen pool of human and animal populations
are intrinsically linked and provides evidence that antibiotic
usage in animal medicine is shaping the population of a major
human pathogen. IMPORTANCE: Methicillin-resistant Staphylococcus
aureus (MRSA) is major problem in human medicine. Companion
animals, such as cats, dogs, and horses, can also become
colonized and infected by MRSA. Here, we demonstrate that a
shared population of an important and globally disseminated
lineage of MRSA can infect both humans and companion animals
without undergoing host adaptation. This suggests that companion
animals might act as a reservoir for human infections. We also
show that the isolates from companion animals have differences in
the presence of certain antibiotic resistance genes. This study
furthers the ``one health'' view of infectious diseases by
demonstrating that the pool of MRSA isolates in the human and
animal populations are shared and highlights how different
antibiotic usage patterns between human and veterinary medicine
can shape the population of bacterial pathogens.",
journal = "MBio",
volume = 5,
number = 3,
pages = "e00985--13",
month = may,
year = 2014,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Warne2016-sf,
title = "The {Ess/Type} {VII} secretion system of Staphylococcus aureus
shows unexpected genetic diversity",
author = "Warne, Ben and Harkins, Catriona P and Harris, Simon R and
Vatsiou, Alexandra and Stanley-Wall, Nicola and Parkhill, Julian
and Peacock, Sharon J and Palmer, Tracy and Holden, Matthew T G",
abstract = "BACKGROUND: Type VII protein secretion (T7SS) is a specialised
system for excreting extracellular proteins across bacterial cell
membranes and has been associated with virulence in
Staphylococcus aureus. The genetic diversity of the ess locus,
which encodes the T7SS, and the functions of proteins encoded
within it are poorly understood. RESULTS: We used whole genome
sequence data from 153 isolates representative of the diversity
of the species to investigate the genetic variability of T7SS
across S. aureus. The ess loci were found to comprise of four
distinct modules based on gene content and relative conservation.
Modules 1 and 4, comprising of the 5' and 3' modules of the ess
locus, contained the most conserved clusters of genes across the
species. Module 1 contained genes encoding the secreted protein
EsxA, and the EsaAB and EssAB components of the T7SS machinery,
and Module 4 contained two functionally uncharacterized conserved
membrane proteins. Across the species four variants of Module 2
were identified containing the essC gene, each of which was
associated with a specific group of downstream genes. The most
diverse module of the ess locus was Module 3 comprising a highly
variable arrangement of hypothetical proteins. RNA-Seq was
performed on representatives of the four Module 2 variants and
demonstrated strain-specific differences in the levels of
transcription in the conserved Module 1 components and
transcriptional linkage Module 2, and provided evidence of the
expression of genes the variable regions of the ess loci.
CONCLUSIONS: The ess locus of S. aureus exhibits modularity and
organisational variation across the species and transcriptional
variation. In silico analysis of ess loci encoded hypothetical
proteins identified potential novel secreted substrates for the
T7SS. The considerable variety in operon arrangement between
otherwise closely related isolates provides strong evidence for
recombination at this locus. Comparison of these recombination
regions with each other, and with the genomes of other
Staphylococcal species, failed to identify evidence of intra- and
inter-species recombination, however the analysis identified a
novel T7SS in another pathogenic staphylococci, Staphylococcus
lugdunensis.",
journal = "BMC Genomics",
volume = 17,
pages = "222",
month = mar,
year = 2016,
keywords = "Secretion; Staphylococcus aureus; Type
VII;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Koskella2014-it,
title = "Bacteria-phage coevolution as a driver of ecological and
evolutionary processes in microbial communities",
author = "Koskella, Britt and Brockhurst, Michael A",
abstract = "Bacteria-phage coevolution, the reciprocal evolution between
bacterial hosts and the phages that infect them, is an important
driver of ecological and evolutionary processes in microbial
communities. There is growing evidence from both laboratory and
natural populations that coevolution can maintain phenotypic and
genetic diversity, increase the rate of bacterial and phage
evolution and divergence, affect community structure, and shape
the evolution of ecologically relevant bacterial traits. Although
the study of bacteria-phage coevolution is still in its infancy,
with open questions regarding the specificity of the interaction,
the gene networks of coevolving partners, and the relative
importance of the coevolving interaction in complex communities
and environments, there have recently been major advancements in
the field. In this review, we sum up our current understanding of
bacteria-phage coevolution both in the laboratory and in nature,
discuss recent findings on both the coevolutionary process itself
and the impact of coevolution on bacterial phenotype, diversity
and interactions with other species (particularly their
eukaryotic hosts), and outline future directions for the field.",
journal = "FEMS Microbiol. Rev.",
volume = 38,
number = 5,
pages = "916--931",
month = sep,
year = 2014,
keywords = "antagonistic; bacteriophage; host-parasite; infection;
resistance; species
interaction;phage;evolution;Staphylococcus;Papers\_for\_Michelle;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{McAdam2011-cn,
title = "Adaptive evolution of Staphylococcus aureus during chronic
endobronchial infection of a cystic fibrosis patient",
author = "McAdam, Paul R and Holmes, Anne and Templeton, Kate E and
Fitzgerald, J Ross",
abstract = "The molecular adaptation of Staphylococcus aureus to its host
during chronic infection is not well understood. Comparative
genome sequencing of 3 S. aureus isolates obtained sequentially
over 26 months from the airways of a cystic fibrosis patient,
revealed variation in phage content, and genetic polymorphisms in
genes which influence antibiotic resistance, and global
regulation of virulence. The majority of polymorphisms were
isolate-specific suggesting the existence of an heterogeneous
infecting population that evolved from a single infecting strain
of S. aureus. The genetic variation identified correlated with
differences in growth rate, hemolytic activity, and antibiotic
sensitivity, implying a profound effect on the ecology of S.
aureus. In particular, a high frequency of mutations in loci
associated with the alternate transcription factor SigB, were
observed. The identification of genes under diversifying
selection during long-term infection may inform the design of
novel therapeutics for the control of refractory chronic
infections.",
journal = "PLoS One",
volume = 6,
number = 9,
pages = "e24301",
month = sep,
year = 2011,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Donker2017-te,
title = "Population genetic structuring of methicillin-resistant
Staphylococcus aureus clone {EMRSA-15} within {UK} reflects
patient referral patterns",
author = "Donker, Tjibbe and Reuter, Sandra and Scriberras, James and
Reynolds, Rosy and Brown, Nicholas M and Est{\'e}e
T{\"o}r{\"o}k, M and James, Richard and {East of England
Microbiology Research Network} and Aanensen, David M and
Bentley, Stephen D and Holden, Matthew T G and Parkhill, Julian
and Spratt, Brian G and Peacock, Sharon J and Feil, Edward J and
Grundmann, Hajo",
abstract = "Antibiotic resistance forms a serious threat to the health of
hospitalised patients, rendering otherwise treatable bacterial
infections potentially life-threatening. A thorough
understanding of the mechanisms by which resistance spreads
between patients in different hospitals is required in order to
design effective control strategies. We measured the differences
between bacterial populations of 52 hospitals in the United
Kingdom and Ireland, using whole-genome sequences from 1085 MRSA
clonal complex 22 isolates collected between 1998 and 2012. The
genetic differences between bacterial populations were compared
with the number of patients transferred between hospitals and
their regional structure. The MRSA populations within single
hospitals, regions and countries were genetically distinct from
the rest of the bacterial population at each of these levels.
Hospitals from the same patient referral regions showed more
similar MRSA populations, as did hospitals sharing many
patients. Furthermore, the bacterial populations from different
time-periods within the same hospital were generally more
similar to each other than contemporaneous bacterial populations
from different hospitals. We conclude that, while a large part
of the dispersal and expansion of MRSA takes place among
patients seeking care in single hospitals, inter-hospital spread
of resistant bacteria is by no means a rare occurrence.
Hospitals are exposed to constant introductions of MRSA on a
number of levels: (1) most MRSA is received from hospitals that
directly transfer large numbers of patients, while (2) fewer
introductions happen between regions or (3) across national
borders, reflecting lower numbers of transferred patients. A
joint coordinated control effort between hospitals, is therefore
paramount for the national control of MRSA, antibiotic-resistant
bacteria and other hospital-associated pathogens.",
journal = "Microbial Genomics",
publisher = "Microbiology Society",
month = jul,
year = 2017,
keywords = "hospital network; antimicrobial Resistance;
MRSA;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{McMillan2017-xh,
title = "Draft Genome Sequences of 15 Staphylococcus aureus Isolates
Recovered from Raw Milk and Associated Milk Filters from
Victoria, Australia",
author = "McMillan, Kate and Allnutt, Theodore R and Fox, Edward M",
abstract = "This study describes draft whole genomes of 15 Staphylococcus
aureus isolates from dairy farms located in Victoria, Australia.
Two novel sequence types (ST3183 and ST3184) were identified
among these isolates.",
journal = "Genome Announc.",
volume = 5,
number = 2,
month = jan,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Franck2017-tn,
title = "Staphylococcal aureus Enterotoxin {C} and {Enterotoxin-Like} {L}
Associated with Post-partum Mastitis",
author = "Franck, Kristina T and Gumpert, Heidi and Olesen, Bente and
Larsen, Anders R and Petersen, Andreas and Bangsborg, Jette and
Albertsen, Per and Westh, Henrik and Bartels, Mette D",
abstract = "Denmark is a low prevalence country with regard to methicillin
resistant Staphylococcus aureus (MRSA). In 2008 and 2014, two
neonatal wards in the Copenhagen area experienced outbreaks with
a typical community acquired MRSA belonging to the same spa type
and sequence type (t015:ST45) and both were PVL and ACME
negative. In outbreak 1, the isolates harbored SCCmec IVa and in
outbreak 2 SCCmec V. The clinical presentation differed between
the two outbreaks, as none of five MRSA positive mothers in
outbreak 1 had mastitis vs. five of six MRSA positive mothers in
outbreak 2 (p < 0.02). To investigate if whole-genome sequencing
could identify virulence genes associated with mastitis,
t015:ST45 isolates from Denmark (N = 101) were whole-genome
sequenced. Sequence analysis confirmed two separate outbreaks
with no sign of sustained spread into the community. Analysis of
the accessory genome between isolates from the two outbreaks
revealed a S. aureus pathogenicity island containing enterotoxin
C and enterotoxin-like L only in isolates from outbreak 2.
Enterotoxin C and enterotoxin-like L carrying S. aureus are
associated with bovine mastitis and our findings indicate that
these may also be important virulence factors for human mastitis.",
journal = "Front. Microbiol.",
volume = 8,
pages = "173",
month = feb,
year = 2017,
keywords = "MRSA; SaPITokyo12571; clinical presentation; enterotoxins;
pathogenicity islands; post-partum mastitis; virulence;
whole-genome
sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Murray2017-uw,
title = "Recombination-mediated host-adaptation by avian Staphylococcus
aureus",
author = "Murray, Susan and Pascoe, Ben and M{\'e}ric, Guillaume and
Mageiros, Leonardos and Yahara, Koji and Hitchings, Matthew D and
Friedmann, Yasmin and Wilkinson, Thomas S and Gormley, Fraser J
and Mack, Dietrich and Bray, James E and Lamble, Sarah and
Bowden, Rory and Jolley, Keith A and Maiden, Martin C J and
Wendlandt, Sarah and Schwarz, Stefan and Corander, Jukka and Ross
Fitzgerald, J and Sheppard, Samuel K",
journal = "Genome Biol. Evol.",
month = feb,
year = 2017,
keywords = "Staphylococcus;recombination;colonization;plasmid;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
}
@ARTICLE{Bakthavatchalam2017-bb,
title = "Draft genome sequence of reduced teicoplanin-susceptible and
vancomycin-heteroresistant methicillin-resistant Staphylococcus
aureus from sepsis cases",
author = "Bakthavatchalam, Yamuna Devi and Veeraraghavan, Balaji and
Devanga Ragupathi, Naveen Kumar and Babu, Priyanka and Munuswamy,
Elakkiya and David, Thambu",
abstract = "Here we report the whole-genome shotgun sequence of six
methicillin-resistant Staphylococcus aureus (MRSA) showing
reduced susceptibility to both vancomycin and teicoplanin. The
typical Indian community-acquired MRSA (CA-MRSA) clone
ST772-MRSA-V-t657 was the most common genotype (3/6; 50\%),
followed by ST672-MRSA-IV (2/6; 33\%) and ST22-MRSA-IV (1/6;
17\%). All strains harboured a mutation in the tcaRAB operon,
vraSR, graSR and/or rpoB genes, which are frequently mutated
determinants in a heteroresistant vancomycin-intermediate S.
aureus (hVISA) phenotype.",
journal = "J Glob Antimicrob Resist",
volume = 8,
pages = "169--171",
month = feb,
year = 2017,
keywords = "MRSA; hVISA;
tcaA;Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Diene2017-oq,
title = "Prophages and adaptation of Staphylococcus aureus {ST398} to the
human clinic",
author = "Diene, Seydina M and Corvaglia, Anna Rita and Fran{\c c}ois,
Patrice and van der Mee-Marquet, Nathalie and {Regional Infection
Control Group of the Centre Region}",
abstract = "BACKGROUND: It has been suggested that prophages in the ST398 S.
aureus clone are responsible for expanding ST398's spectrum of
action and increasing its ability to cause human infections. We
carried out the first characterization of the various prophages
carried by 76 ST398 bloodstream infection (BSI) isolates obtained
over 9 years of observation. RESULTS: Whole-genome sequencing of
22 representative isolates showed (1) the presence of the
$\varphi$3-prophage and diverse genetic features typical of
animal-associated isolates (i.e., SCCmec XI element, Tn916
transposon and non $\varphi$3-prophages) in a majority of BSI
isolates, (2) one BSI isolate devoid of the $\varphi$3-prophage
but otherwise similar to an animal-infecting isolate, (3) 35
prophages carrying numerous genes previously associated with
virulence or immune evasion in animal models of staphylococcal
infections. The analysis of prophage content in all 76 BSI
isolates showed an increasing prevalence of polylysogeny over
time. Overall, over the course of the last 10 years, the BSI
isolates appear to have acquired increasing numbers of genetic
features previously shown to contribute to bacterial adaptation
and virulence in animal models of staphylococcal infections.
CONCLUSIONS: We hypothesize that lysogeny has played a
significant role in increasing the ability of the ST398 clone to
cause infections in humans. Our findings highlight the risk that
the ST398 lineage will increase its threat to public health by
continuing to acquire virulence and/or multiple
antibiotic-resistance genes from hospital-associated clones of
Staphylococcus aureus.",
journal = "BMC Genomics",
volume = 18,
number = 1,
pages = "133",
month = feb,
year = 2017,
keywords = "Bloodstream infections; CC398 lineage; Evolution;
Livestock-associated; Phage content; Prophage; Staphylococcus
aureus;
$\varphi$3-prophage;Staphylococcus;phage;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human",
language = "en"
}
@ARTICLE{Mannala2017-tj,
title = "Complete Genome and Plasmid Sequences of \textit{Staphylococcus
aureus} {EDCC} 5055 ({DSM} 28763), Used To Study
{Implant-Associated} Infections",
author = "Mannala, Gopala Krishna and Hain, Torsten and Spr{\"o}er, Cathrin
and Bunk, Boyke and Overmann, J{\"o}rg and Alt, Volker and
Domann, Eugen",
abstract = "Staphylococcus aureus EDCC 5055 (DSM 28763) is a human clinical
wound isolate intensively used to study implant-associated
infections in rabbit and rat infection models. Here, we report
its complete genome sequence (2,794,437 bp) along with that of
one plasmid (27,437 bp). This strain belongs to sequence type 8
and contains a mecA gene.",
journal = "Genome Announc.",
volume = 5,
number = 8,
month = feb,
year = 2017,
keywords = "Staphylococcus;plasmid;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Kpeli2017-lk,
title = "Genomic analysis of {ST88} community-acquired methicillin
resistant \textit{Staphylococcus aureus} in Ghana",
author = "Kpeli, Grace and Buultjens, Andrew H and Giulieri, Stefano and
Owusu-Mireku, Evelyn and Aboagye, Samuel Y and Baines, Sarah L
and Seemann, Torsten and Bulach, Dieter and Gon{\c c}alves da
Silva, Anders and Monk, Ian R and Howden, Benjamin P and
Pluschke, Gerd and Yeboah-Manu, Dorothy and Stinear, Timothy",
abstract = "BACKGROUND: The emergence and evolution of community-acquired
methicillin resistant Staphylococcus aureus (CA-MRSA) strains in
Africa is poorly understood. However, one particular MRSA lineage
called ST88, appears to be rapidly establishing itself as an
``African'' CA-MRSA clone. In this study, we employed whole
genome sequencing to provide more information on the genetic
background of ST88 CA-MRSA isolates from Ghana and to describe in
detail ST88 CA-MRSA isolates in comparison with other MRSA
lineages worldwide. METHODS: We first established a complete ST88
reference genome (AUS0325) using PacBio SMRT sequencing. We then
used comparative genomics to assess relatedness among 17 ST88
CA-MRSA isolates recovered from patients attending Buruli ulcer
treatment centres in Ghana, three non-African ST88s and 15 other
MRSA lineages. RESULTS: We show that Ghanaian ST88 forms a
discrete MRSA lineage (harbouring SCCmec-IV [2B]). Gene content
analysis identified five distinct genomic regions enriched among
ST88 isolates compared with the other S. aureus lineages. The
Ghanaian ST88 isolates had only 658 core genome SNPs and there
was no correlation between phylogeny and geography, suggesting
the recent spread of this clone. The lineage was also resistant
to multiple classes of antibiotics including $\beta$-lactams,
tetracycline and chloramphenicol. DISCUSSION: This study reveals
that S. aureus ST88-IV is a recently emerging and rapidly
spreading CA-MRSA clone in Ghana. The study highlights the
capacity of small snapshot genomic studies to provide actionable
public health information in resource limited settings. To our
knowledge this is the first genomic assessment of the ST88
CA-MRSA clone.",
journal = "PeerJ",
volume = 5,
pages = "e3047",
month = feb,
year = 2017,
keywords = "CA-MRSA; Comparative genomics; MRSA; Phylogeography; ST88;
Staphylococcus aureus; Whole genome
sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Piso2017-yj,
title = "A {Cross-Sectional} Study of Colonization Rates with
{Methicillin-Resistant} Staphylococcus aureus ({MRSA}) and
{Extended-Spectrum} {Beta-Lactamase} ({ESBL}) and
{Carbapenemase-Producing} Enterobacteriaceae in Four Swiss
Refugee Centres",
author = "Piso, Rein Jan and K{\"a}ch, Roman and Pop, Roxana and Zillig,
Daniela and Schibli, Urs and Bassetti, Stefano and Meinel,
Dominik and Egli, Adrian",
abstract = "BACKGROUND: The recent crisis of refugees seeking asylum in
European countries challenges public health on many levels. Most
refugees currently arrive from Syria, Afghanistan, or Eritrea.
Data about multidrug resistant bacteria (MDR) prevalence are not
present for these countries. However, when entering the European
heath care systems, data about colonisation rates regarding
highly resistant bacterial pathogens are important. METHODS: We
performed a cross-sectional screening in four Swiss refugee
centres to determine the colonization rates for MRSA and ESBL-
and carbapenemase-producing Enterobacteriaceae. We used
pharyngeal, nasal, and inguinal swabs for MRSA and rectal swabs
and urine for ESBL and carbapenemase screening using standard
microbiological procedures. Whole genome sequencing (WGS) was
used to determine the relatedness of MRSA isolates with high
resolution due to a suspected outbreak. RESULTS: 41/261(15.7\%)
refugees were colonized with MRSA. No differences regarding the
country of origin were observed. However, in a single centre
significantly more were colonized, which was confirmed to be a
recent local outbreak. 57/241 (23.7\%) refugees were colonized
with ESBL with significantly higher colonisation in persons
originating from the Middle East (35.1\%, p<0.001). No
carbapenemase producers were detected. CONCLUSION: The
colonisation rate of the refugees was about 10 times higher for
MRSA and 2-5 times higher for ESBL compared to the Swiss
population. Contact precaution is warranted for these persons if
they enter medical care. In cases of infections, MRSA and
ESBL-producing Enterobacteriaceae should be considered regarding
antibiotic treatment choices.",
journal = "PLoS One",
volume = 12,
number = 1,
pages = "e0170251",
month = jan,
year = 2017,
keywords = "Staphylococcus;antibiotics;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@UNPUBLISHED{Young2017-di,
title = "Severe infections emerge from the microbiome by adaptive
evolution",
author = "Young, Bernadette C and Wu, Chieh-Hsi and Claire Gordon, N and
Cole, Kevin and Price, James R and Liu, Elian and Sheppard, Anna
and Perera, Sanuki and Charlesworth, Jane and Golubchik, Tanya
and Iqbal, Zamin and Bowden, Rory and Massey, Ruth and Paul, John
and Crook, Derrick W and Peto, Timothy E A and Sarah Walker, A
and Llewelyn, Martin and Wyllie, David H and Wilson, Daniel",
abstract = "Bacteria responsible for the greatest global mortality colonize
the human microbiome far more frequently than they cause severe
infections. Whether mutation and selection within the microbiome
precipitate infection is unknown. To address this question, we
investigated de novo mutation in 1163 Staphylococcus aureus
genomes from 105 infected patients with nose-colonization. We
report that 72\% of the infections emerged from the microbiome,
with infecting and nose-colonizing bacteria showing systematic
adaptive differences. We found 3.6-fold, 2.9-fold and 2.8-fold
enrichments of protein-altering variants in genes responding to
rsp, which regulates surface antigens and toxicity; agr, which
regulates quorum-sensing, toxicity and abscess formation; and
host-derived antimicrobial peptides, respectively. These adaptive
signatures were not observed in healthy carriers and differed
from prevailing species-level signals of selection, suggesting
disease-associated, short-term, within-host selection pressures.
Our results show that infection, like a cancer of the microbiome,
emerges through spontaneous adaptive evolution, raising new
possibilities for diagnosis and treatment.",
journal = "bioRxiv",
pages = "116681",
month = mar,
year = 2017,
keywords = "microbiome;Staphylococcus;evolution;systems\_biology;confirmed\_SA-resistance-mutation;within-host-evolution;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Murray2017-if,
title = "Recombination-mediated host-adaptation by avian Staphylococcus
aureus",
author = "Murray, Susan and Pascoe, Ben and M{\'e}ric, Guillaume and
Mageiros, Leonardos and Yahara, Koji and Hitchings, Matthew D and
Friedmann, Yasmin and Wilkinson, Thomas S and Gormley, Fraser J
and Mack, Dietrich and Bray, James E and Lamble, Sarah and
Bowden, Rory and Jolley, Keith A and Maiden, Martin C J and
Wendlandt, Sarah and Schwarz, Stefan and Corander, Jukka and Ross
Fitzgerald, J and Sheppard, Samuel K",
abstract = "Staphylococcus aureus are globally disseminated among farmed
chickens causing skeletal muscle infections, dermatitis and
septicaemia. The emergence of poultry-associated lineages has
involved zoonotic transmission from humans to chickens but
questions remain about the specific adaptations that promote
proliferation of chicken pathogens. We characterised genetic
variation in a population of genome-sequenced S. aureus isolates
of poultry and human origin. Genealogical analysis identified a
dominant poultry-associated sequence cluster within the CC5
clonal complex. Poultry and human CC5 isolates were significantly
distinct from each other and more recombination events were
detected in the poultry isolates. We identified forty-four
recombination events in 33 genes along the branch extending to
the poultry-specific CC5 cluster, and 47 genes were found more
often in CC5 poultry isolates compared to those from humans. Many
of these gene sequences were common in chicken isolates from
other clonal complexes suggesting horizontal gene transfer among
poultry associated lineages. Consistent with functional
predictions for putative poultry-associated genes, poultry
isolates showed enhanced growth at 42oC and greater erythrocyte
lysis on chicken blood agar in comparison with human isolates. By
combining phenotype information with evolutionary analysis of
staphylococcal genomes, we provide evidence of adaptation,
following a human-to-poultry host transition. This has important
implications for the emergence and dissemination of new
pathogenic clones associated with modern agriculture.",
journal = "Genome Biol. Evol.",
month = feb,
year = 2017,
keywords = "Evolution; Genomics; Poultry infection; Recombination;
Staphylococcus;Staphylococcus;recombination;colonization;plasmid;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human",
language = "en"
}
% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Bayliss2017-kb,
title = "The use of Oxford Nanopore native barcoding for complete genome
assembly",
author = "Bayliss, Sion C and Hunt, Vicky L and Yokoyama, Maho and Thorpe,
Harry A and Feil, Edward J",
abstract = "Background: The Oxford Nanopore Technologies MinION(TM) is a
mobile DNA sequencer that can produce long read sequences with a
short turn-around time. Here we report the first demonstration of
single contig genome assembly using Oxford Nanopore native
barcoding when applied to a multiplexed library of 12 samples and
combined with existing Illumina short-read data. This paves the
way for the closure of multiple bacterial genomes from a single
MinION(TM) sequencing run, given the availability of existing
short-read data. The strain we used, MHO\_001, represents the
important community-acquired methicillin resistant Staphylococcus
aureus lineage USA300. Findings: Using a hybrid assembly of
existing short read and barcoded long read sequences from
multiplexed data, we completed a genome of the S. aureus USA300
strain MHO\_001. The long-read data represented only ∼5-10\% of
an average MinION(TM) run (∼7x genomic coverage), but, using
standard tools, this was sufficient to complete the circular
chromosome of S. aureus strain MHO\_001 (2.86 Mb) and two
complete plasmids (27 Kb and 3 Kb). Minor differences were noted
when compared to USA300 reference genome, USA300\_FPR3757,
including the translocation, loss and gain of mobile genetic
elements. Conclusion: Here we demonstrate that MinION(TM) reads,
multiplexed using native barcoding, can be used in combination
with short-read data, to fully complete a bacterial genome. The
ability to complete multiple genomes, for which short-read data
is already available, from a single MinION(TM) run is set to
impact on our understanding of accessory genome content, plasmid
diversity and genome rearrangements.",
journal = "Gigascience",
month = feb,
year = 2017,
keywords = "MinION; Staphylococcus aureus; Whole genome sequencing; bacterial
genomics; hybrid assembly; long read; multiplexing; native
barcoding;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Hau2017-cu,
title = "Draft Genome Sequences of 14 \textit{Staphylococcus aureus}
Sequence Type 5 Isolates from California, {USA}",
author = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and
Nicholson, Tracy L",
abstract = "Staphylococcus aureus is part of the human epithelial microbiota;
however, it is also a pathogen. The acquisition of mobile genetic
elements plays a role in the virulence of S. aureus isolates and
contributes to treatment failures. This report details the draft
genome sequences of 14 clinical S. aureus isolates.",
journal = "Genome Announc.",
volume = 5,
number = 13,
month = mar,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Hau2017-yd,
title = "Complete Genome Sequences of Two \textit{Staphylococcus aureus}
Sequence Type 5 Isolates from California, {USA}",
author = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and
Nicholson, Tracy L",
abstract = "Staphylococcus aureus causes a variety of human diseases ranging
in severity. The pathogenicity of S. aureus can be partially
attributed to the acquisition of mobile genetic elements. In this
report, we provide two complete genome sequences from human
clinical S. aureus isolates.",
journal = "Genome Announc.",
volume = 5,
number = 13,
month = mar,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Balachandran2017-ld,
title = "Complete Genome Sequence of \textit{Staphylococcus aureus} Strain
Wood 46",
author = "Balachandran, Manasi and Riley, Matthew C and Bemis, David A and
Kania, Stephen A",
abstract = "Here, we report the first complete genome sequence of the
Staphylococcus aureus strain Wood 46. Wood 46 has played an
important role in understanding the virulence and pathogenesis of
S. aureus infections. This report will assist efforts in vaccine
development against methicillin-resistant S. aureus (MRSA)
infections.",
journal = "Genome Announc.",
volume = 5,
number = 13,
month = mar,
year = 2017,
keywords = "Staphylococcus;phage;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Lin2017-aq,
title = "Nucleotide Sequence Variations in Autolysis Genes of {ST} 59
{Methicillin-Resistant} Staphylococcus aureus Isolates",
author = "Lin, Lee-Chung and Shu, Jwu-Ching and Chang, Shih-Cheng and Ge,
Mao-Cheng and Liu, Tsui-Ping and Chen, Chien-Wei and Lu, Jang-Jih",
abstract = "Biofilm formation is a virulence factor of bacteria. The goal of
this study was to understand the mechanisms of biofilm formation
by methicillin-resistant Staphylococcus aureus (MRSA).
Whole-genome sequencing of eight MRSA strains was performed to
identify sequence variations in genes related to biofilm
formation. Thirty-one genes involved in MRSA biofilm formation
were analyzed and 11 amino acid sequence variations in four genes
related to autolysis were found. These variations include E121D
and H387 N in ArlS; Q117K, T424S, K428T, A509S, V752E, A754V, and
T771A in Atl; T184K in CidC; and D251N in CidR. Among the 26
clinical MRSA isolates studied, 13 isolates were nonbiofilm
producers and were found to harbor these mutations. Furthermore,
all of these 13 isolates belonged to ST59. Ten of these 13 ST59
isolates became able to produce biofilms when they were incubated
with extracellular DNA from MRSA N315. Results of this study
suggest that sequence variations in arlS, atl, cidC, and cidR
genes may render MRSA unable to produce biofilms. Further
investigations are needed to correlate these sequence variations
with the biofilm-forming ability of MRSA isolates.",
journal = "Microb. Drug Resist.",
month = mar,
year = 2017,
keywords = "MRSA; ST59; biofilm;
eDNA;Staphylococcus;phage;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Tosas_Auguet2016-co,
title = "Evidence for Community Transmission of {Community-Associated} but
Not {Health-Care-Associated} {Methicillin-Resistant}
Staphylococcus Aureus Strains Linked to Social and Material
Deprivation: Spatial Analysis of Cross-sectional Data",
author = "Tosas Auguet, Olga and Betley, Jason R and Stabler, Richard A and
Patel, Amita and Ioannou, Avgousta and Marbach, Helene and Hearn,
Pasco and Aryee, Anna and Goldenberg, Simon D and Otter, Jonathan
A and Desai, Nergish and Karadag, Tacim and Grundy, Chris and
Gaunt, Michael W and Cooper, Ben S and Edgeworth, Jonathan D and
Kypraios, Theodore",
abstract = "BACKGROUND: Identifying and tackling the social determinants of
infectious diseases has become a public health priority following
the recognition that individuals with lower socioeconomic status
are disproportionately affected by infectious diseases. In many
parts of the world, epidemiologically and genotypically defined
community-associated (CA) methicillin-resistant Staphylococcus
aureus (MRSA) strains have emerged to become frequent causes of
hospital infection. The aim of this study was to use spatial
models with adjustment for area-level hospital attendance to
determine the transmission niche of genotypically defined CA- and
health-care-associated (HA)-MRSA strains across a diverse region
of South East London and to explore a potential link between MRSA
carriage and markers of social and material deprivation. METHODS
AND FINDINGS: This study involved spatial analysis of
cross-sectional data linked with all MRSA isolates identified by
three National Health Service (NHS) microbiology laboratories
between 1 November 2011 and 29 February 2012. The cohort of
hospital-based NHS microbiology diagnostic services serves
867,254 usual residents in the Lambeth, Southwark, and Lewisham
boroughs in South East London, United Kingdom (UK). Isolates were
classified as HA- or CA-MRSA based on whole genome sequencing.
All MRSA cases identified over 4 mo within the three-borough
catchment area (n = 471) were mapped to small geographies and
linked to area-level aggregated socioeconomic and demographic
data. Disease mapping and ecological regression models were used
to infer the most likely transmission niches for each MRSA
genetic classification and to describe the spatial epidemiology
of MRSA in relation to social determinants. Specifically, we
aimed to identify demographic and socioeconomic population traits
that explain cross-area extra variation in HA- and CA-MRSA
relative risks following adjustment for hospital attendance data.
We explored the potential for associations with the English
Indices of Deprivation 2010 (including the Index of Multiple
Deprivation and several deprivation domains and subdomains) and
the 2011 England and Wales census demographic and socioeconomic
indicators (including numbers of households by deprivation
dimension) and indicators of population health. Both CA-and
HA-MRSA were associated with household deprivation (CA-MRSA
relative risk [RR]: 1.72 [1.03-2.94]; HA-MRSA RR: 1.57
[1.06-2.33]), which was correlated with hospital attendance
(Pearson correlation coefficient [PCC] = 0.76). HA-MRSA was also
associated with poor health (RR: 1.10 [1.01-1.19]) and residence
in communal care homes (RR: 1.24 [1.12-1.37]), whereas CA-MRSA
was linked with household overcrowding (RR: 1.58 [1.04-2.41]) and
wider barriers, which represent a combined score for household
overcrowding, low income, and homelessness (RR: 1.76
[1.16-2.70]). CA-MRSA was also associated with recent immigration
to the UK (RR: 1.77 [1.19-2.66]). For the area-level variation in
RR for CA-MRSA, 28.67\% was attributable to the spatial
arrangement of target geographies, compared with only 0.09\% for
HA-MRSA. An advantage to our study is that it provided a
representative sample of usual residents receiving care in the
catchment areas. A limitation is that relationships apparent in
aggregated data analyses cannot be assumed to operate at the
individual level. CONCLUSIONS: There was no evidence of community
transmission of HA-MRSA strains, implying that HA-MRSA cases
identified in the community originate from the hospital reservoir
and are maintained by frequent attendance at health care
facilities. In contrast, there was a high risk of CA-MRSA in
deprived areas linked with overcrowding, homelessness, low
income, and recent immigration to the UK, which was not
explainable by health care exposure. Furthermore, areas adjacent
to these deprived areas were themselves at greater risk of
CA-MRSA, indicating community transmission of CA-MRSA. This
ongoing community transmission could lead to CA-MRSA becoming the
dominant strain types carried by patients admitted to hospital,
particularly if successful hospital-based MRSA infection control
programmes are maintained. These results suggest that community
infection control programmes targeting transmission of CA-MRSA
will be required to control MRSA in both the community and
hospital. These epidemiological changes will also have
implications for effectiveness of risk-factor-based hospital
admission MRSA screening programmes.",
journal = "PLoS Med.",
volume = 13,
number = 1,
pages = "e1001944",
month = jan,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@UNPUBLISHED{Kanjilal2017-av,
title = "Increasing Antibiotic Susceptibility In Staphylococcus aureus In
Boston, Massachusetts, 2000-2014: An Observational Study",
author = "Kanjilal, Sanjat and Sater, Mohamad and Thayer, Maile and
Lagoudas, Georgia and Kim, Soohong and Blainey, Paul and Grad,
Yonatan",
abstract = "Background: Methicillin resistant S. aureus (MRSA) has been
declining over the past decade, but changes in S. aureus overall
and the implications for trends in antibiotic resistance remain
unclear. Objective: To determine whether the decline in rates of
infection by MRSA has been accompanied by changes in rates of
infection by methicillin susceptible, penicillin resistant S.
aureus (MSSA) and penicillin susceptible S. aureus (PSSA). We
test if these dynamics are associated with specific genetic
lineages and evaluate gains and losses of resistance at the
strain level. Methods: We conducted a 15 year retrospective
observational study at two tertiary care institutions in Boston,
MA of 31,589 adult inpatients with S. aureus infections.
Surveillance swabs and duplicate specimens were excluded. We also
sequenced a sample of contemporary isolates (n = 180) obtained
between January 2016 and July 2016. We determined changes in the
annual rates of infection per 1,000 inpatient admissions by S.
aureus subtype and in the annual mean antibiotic resistance by
subtype. We performed phylogenetic analysis to generate a
population structure and infer gain and loss of the genetic
determinants of resistance. Results: Of the 43,954 S. aureus
infections over the study period, 21,779 were MRSA, 17,565 MSSA
and 4,610 PSSA. After multivariate adjustment, annual rates of
infection by S. aureus declined from 2003 to 2014 by 2.9\% (95\%
CI, 1.6\%-4.3\%), attributable to an annual decline in MRSA of
9.1\% (95\% CI, 6.3\%-11.9\%) and in MSSA by 2.2\% (95\% CI,
0.4\%-4.0\%). PSSA increased over this time period by 4.6\% (95\%
CI, 3.0\%-6.3\%) annually. Resistance in S. aureus decreased from
2000 to 2014 by 0.86 antibiotics (95\% CI, 0.81-0.91). By
phylogenetic inference, 5/35 MSSA and 2/20 PSSA isolates in the
common MRSA lineages ST5/USA100 and ST8/USA300 arose from the
loss of genes conferring resistance. Conclusions and relevance:
At two large tertiary care centers in Boston, MA, S. aureus
infections have decreased in rate and have become more
susceptible to antibiotics, with a rise in PSSA making penicillin
an increasingly viable and important treatment option.",
journal = "bioRxiv",
pages = "125369",
month = apr,
year = 2017,
keywords = "Staphylococcus;antibiotics;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{De_Carvalho2017-rz,
title = "Draft Genome Sequences of Two Clinical {Methicillin-Resistant}
\textit{Staphylococcus aureus} Strains Isolated from Healthy
Children in Brazil",
author = "de Carvalho, Suzi P and de Almeida, J{\'e}ssica B and de Freitas,
Leandro M and Guimaraes, Ana Marcia S and do Nascimento,
Na{\'\i}la C and Dos Santos, Andrea P and Messick, Joanne B and
Timenetsky, Jorge and Marques, Lucas M",
abstract = "We report here the draft genome sequences of two
community-associated methicillin-resistant Staphylococcus aureus
(CA-MRSA) strains, C18 and C80, isolated from healthy children
from day care centers. To our knowledge, these are the first
draft genome sequences of CA-MRSA ST398/CC398/SccmecV and CA-MRSA
ST5/CC5/SccmecIVa isolated from healthy children in Brazil.",
journal = "Genome Announc.",
volume = 5,
number = 15,
month = apr,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Earls2017-dk,
title = "The recent emergence in hospitals of multidrug-resistant
community-associated sequence type 1 and spa type t127
methicillin-resistant Staphylococcus aureus investigated by
whole-genome sequencing: Implications for screening",
author = "Earls, Megan R and Kinnevey, Peter M and Brennan, Gr{\'a}inne I
and Lazaris, Alexandros and Skally, Mairead and O'Connell, Brian
and Humphreys, Hilary and Shore, Anna C and Coleman, David C",
abstract = "Community-associated spa type t127/t922 methicillin-resistant
Staphylococcus aureus (MRSA) prevalence increased from 1\%-7\% in
Ireland between 2010-2015. This study tracked the spread of 89
such isolates from June 2013-June 2016. These included 78
healthcare-associated and 11 community associated-MRSA isolates
from a prolonged hospital outbreak (H1) (n = 46), 16 other
hospitals (n = 28), four other healthcare facilities (n = 4) and
community-associated sources (n = 11). Isolates underwent
antimicrobial susceptibility testing, DNA microarray profiling
and whole-genome sequencing. Minimum spanning trees were
generated following core-genome multilocus sequence typing and
pairwise single nucleotide variation (SNV) analysis was
performed. All isolates were sequence type 1 MRSA staphylococcal
cassette chromosome mec type IV (ST1-MRSA-IV) and 76/89 were
multidrug-resistant. Fifty isolates, including 40/46 from H1,
were high-level mupirocin-resistant, carrying a conjugative 39 kb
iles2-encoding plasmid. Two closely related ST1-MRSA-IV strains
(I and II) and multiple sporadic strains were identified. Strain
I isolates (57/89), including 43/46 H1 and all high-level
mupirocin-resistant isolates, exhibited $\leq$80 SNVs. Two strain
I isolates from separate H1 healthcare workers differed from
other H1/strain I isolates by 7-47 and 12-53 SNVs, respectively,
indicating healthcare worker involvement in this outbreak. Strain
II isolates (19/89), including the remaining H1 isolates,
exhibited $\leq$127 SNVs. For each strain, the pairwise SNVs
exhibited by healthcare-associated and community-associated
isolates indicated recent transmission of ST1-MRSA-IV within and
between multiple hospitals, healthcare facilities and communities
in Ireland. Given the interchange between healthcare-associated
and community-associated isolates in hospitals, the risk factors
that inform screening for MRSA require revision.",
journal = "PLoS One",
volume = 12,
number = 4,
pages = "e0175542",
month = apr,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Rolo2017-tl,
title = "Evidence for the evolutionary steps leading to mecA-mediated
$\beta$-lactam resistance in staphylococci",
author = "Rolo, Joana and Worning, Peder and Boye Nielsen, Jesper and
Sobral, Rita and Bowden, Rory and Bouchami, Ons and Damborg,
Peter and Guardabassi, Luca and Perreten, Vincent and Westh,
Henrik and Tomasz, Alexander and de Lencastre, Herm{\'\i}nia and
Miragaia, Maria",
abstract = "The epidemiologically most important mechanism of antibiotic
resistance in Staphylococcus aureus is associated with mecA-an
acquired gene encoding an extra penicillin-binding protein
(PBP2a) with low affinity to virtually all $\beta$-lactams. The
introduction of mecA into the S. aureus chromosome has led to the
emergence of methicillin-resistant S. aureus (MRSA) pandemics,
responsible for high rates of mortality worldwide. Nonetheless,
little is known regarding the origin and evolution of mecA.
Different mecA homologues have been identified in species
belonging to the Staphylococcus sciuri group representing the
most primitive staphylococci. In this study we aimed to identify
evolutionary steps linking these mecA precursors to the
$\beta$-lactam resistance gene mecA and the resistance phenotype.
We sequenced genomes of 106 S. sciuri, S. vitulinus and S.
fleurettii strains and determined their oxacillin susceptibility
profiles. Single-nucleotide polymorphism (SNP) analysis of the
core genome was performed to assess the genetic relatedness of
the isolates. Phylogenetic analysis of the mecA gene homologues
and promoters was achieved through nucleotide/amino acid sequence
alignments and mutation rates were estimated using a Bayesian
analysis. Furthermore, the predicted structure of mecA
homologue-encoded PBPs of oxacillin-susceptible and -resistant
strains were compared. We showed for the first time that
oxacillin resistance in the S. sciuri group has emerged multiple
times and by a variety of different mechanisms. Development of
resistance occurred through several steps including structural
diversification of the non-binding domain of native PBPs; changes
in the promoters of mecA homologues; acquisition of SCCmec and
adaptation of the bacterial genetic background. Moreover, our
results suggest that it was exposure to $\beta$-lactams in
human-created environments that has driven evolution of native
PBPs towards a resistance determinant. The evolution of
$\beta$-lactam resistance in staphylococci highlights the
numerous resources available to bacteria to adapt to the
selective pressure of antibiotics.",
journal = "PLoS Genet.",
volume = 13,
number = 4,
pages = "e1006674",
month = apr,
year = 2017,
keywords = "Staphylococcus;evolution;antibiotics;oxacillin;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{De_Almeida2017-qf,
title = "Draft Genome Sequence of {Methicillin-Resistant}
\textit{Staphylococcus aureus} Strain {LC33} Isolated from Human
Breast Milk",
author = "de Almeida, J{\'e}ssica B and de Carvalho, Suzi P and de Freitas,
Leandro M and Guimar{\~a}es, Ana Marcia S and do Nascimento,
Na{\'\i}la C and Dos Santos, Andrea P and Messick, Joanne B and
Timenetsky, Jorge and Marques, Lucas M",
abstract = "Here, we report the draft genome sequence of Staphylococcus
aureus strain LC33, isolated from human breast milk in Brazil.
This microorganism has been typed as ST1/t127/sccmecV. To our
knowledge, this is the first draft genome sequence of a
methicillin-resistant S. aureus strain isolated from human breast
milk.",
journal = "Genome Announc.",
volume = 5,
number = 15,
month = apr,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Cunningham2017-vi,
title = "Comparison of Two {Whole-Genome} Sequencing Methods for Analysis
of Three {Methicillin-Resistant} \textit{Staphylococcus aureus}
Outbreaks",
author = "Cunningham, Scott A and Chia, Nicholas and Jeraldo, Patricio R
and Quest, Daniel J and Johnson, Julie A and Boxrud, Dave J and
Taylor, Angela J and Chen, Jun and Jenkins, Gregory D and
Drucker, Travis M and Nelson, Heidi and Patel, Robin",
abstract = "Whole genome sequencing (WGS) can provide excellent resolution in
global and local epidemiological investigations of Staphylococcus
aureus outbreaks. A variety of sequencing approaches and
analytical tools have been used; it is not clear which is ideal.
We compared two WGS strategies and two analytical approaches to
the standard method of SmaI restriction digestion pulsed-field
gel electrophoresis (PFGE) for typing S. aureus Forty-two S.
aureus isolates from three outbreaks and 12 reference isolates
were studied. Near-complete genomes, assembled de novo with
paired-end and long mate pair (8 Kb) libraries were first
assembled and analyzed utilizing an in-house assembly and
analytical informatics pipeline. In addition, paired-end data was
assembled and analyzed using a commercial software package.
Single nucleotide variant (SNP) analysis was performed using the
in-house pipeline. Two assembly strategies were used to generate
core genome multi-locus sequence typing (cgMLST) data. First, the
near-complete genome data generated with the in-house pipeline
was imported into the commercial software and used to perform
cgMLST analysis. Second, the commercial software was used to
assemble paired-end data and resolved assemblies were used to
perform cgMLST. Similar isolate clustering was observed using SNP
calling and cgMLST, regardless of data assembly strategy. All
methods provided more discrimination between outbreaks than did
PFGE. Overall, all of the evaluated WGS strategies yielded
statistically similar results for S. aureus typing.",
journal = "J. Clin. Microbiol.",
month = apr,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Millar2017-sn,
title = "Genomic Characterization of {USA300} {MRSA} to Evaluate
Intraclass Transmission and Recurrence of {SSTI} among High Risk
Military Trainees",
author = "Millar, Eugene V and Rice, Gregory K and Elassal, Emad M and
Schlett, Carey D and Bennett, Jason W and Redden, Cassie L and
Mor, Deepika and Law, Natasha N and Tribble, David R and
Hamilton, Theron and Ellis, Michael W and Bishop-Lilly, Kimberly
A",
abstract = "Background.: Military trainees are at increased risk for
methicillin-resistant Staphylococcus aureus (MRSA) skin and soft
tissue infection (SSTI). Whole genome sequencing (WGS) can refine
our understanding of MRSA transmission and microevolution in
congregate settings. Methods.: We conducted a prospective
case-control study of SSTI among US Army Infantry trainees at
Fort Benning, GA from July 2012-December 2014. We identified
clusters of USA300 MRSA SSTI within select training classes and
performed WGS on clinical isolates. We then linked genomic,
phylogenetic data, epidemiologic, and clinical data in order to
evaluate intra- and interclass disease transmission. Furthermore,
among cases of recurrent MRSA SSTI, we evaluated the intrahost
relatedness of infecting strains. Results.: Nine training classes
with $\geq$5 cases of USA300 MRSA SSTI were selected. Eighty
USA300 MRSA clinical isolates from 74 trainees, six (8.1\%) of
whom had recurrent infection, were subjected to WGS. We
identified 2719 single nucleotide variants (SNV). The overall
median (range) SNV difference between isolates was 173 (1-339).
Intraclass median SNV differences ranged from 23 to 245. Two
phylogenetic clusters were suggestive of interclass MRSA
transmission. One of these clusters stemmed from two classes that
were separated by a 13-month period but housed in the same
barracks. Among trainees with recurrent MRSA SSTI, the intrahost
median SNV difference was 7.5 (1-48). Conclusions.: Application
of WGS revealed intra- and interclass transmission of MRSA among
military trainees. An interclass cluster between two
non-contemporaneous classes suggests a long-term reservoir for
MRSA in this setting.",
journal = "Clin. Infect. Dis.",
month = apr,
year = 2017,
keywords = "Methicillin-resistant Staphylococcus aureus (MRSA); genomic
epidemiology; military; skin and soft tissue infection; whole
genome
sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Moon2016-be,
title = "Draft Genome Sequences of a Unique {t324-ST541-V}
{Methicillin-Resistant} Staphylococcus aureus Strain from a Pig",
author = "Moon, Dong Chan and Kim, Byung-Yong and Nam, Hyang-Mi and Jang,
Geum-Chan and Jung, Suk-Chan and Lee, Hee-Soo and Park, Yong-Ho
and Lim, Suk-Kyung",
abstract = "Methicillin-resistant Staphylococcus aureus (MRSA), the major
causative agent of nosocomial infection, has also been reported
from non-human sources. A sequence type (ST) 541 MRSA isolate
designated K12PJN53 was isolated from a healthy pig in 2012. The
genome of K12PJN53 consists of 44 contiguous sequences (contigs),
totalling 2,880,108 bases with 32.88\% GC content. Among the
annotated contigs, 14, 17, and 18 contained genes related to
antimicrobial resistance, adherence, and toxin genes,
respectively. The genomic distance of strain K12PJN53 was close
to the ST398 strains. This is the first report of the draft
genome sequence of a novel livestock-associated MRSA ST541
strain.",
journal = "J. Microbiol. Biotechnol.",
volume = 26,
number = 4,
pages = "799--805",
month = apr,
year = 2016,
keywords = "Genomics; MRSA;
Pig;Staphylococcus;antibiotics;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Gordon2017-um,
title = "Whole Genome Sequencing reveals the contribution of long-term
carriers in Staphylococcus aureus outbreak investigation",
author = "Gordon, N C and Pichon, B and Golubchik, T and Wilson, D J and
Paul, J and Blanc, D S and Cole, K and Collins, J and Cortes, N
and Cubbon, M and Gould, F K and Jenks, P J and Llewelyn, M and
Nash, J Q and Orendi, J M and Paranthaman, K and Price, J and
Senn, L and Thomas, H L and Wyllie, S and Crook, D W and Peto, T
E A and Walker, A S and Kearns, A M",
abstract = "Whole genome sequencing (WGS) makes it possible to determine the
relatedness of bacterial isolates at high resolution, helping to
characterise outbreaks. However, for Staphylococcus aureus,
accumulation of within-host diversity during carriage might limit
interpretation of sequencing data.In this study, we hypothesised
the converse: that within-host diversity can in fact be exploited
to reveal the involvement of long-term carriers (LTCs) in
outbreaks. We analysed WGS data from 20 historical outbreaks, and
applied phylogenetic methods to assess genetic relatedness and
estimate time to most recent common ancestor (TMRCA). Findings
were compared with the routine investigation results and
epidemiological evidence.Outbreaks with epidemiological evidence
for an LTC source had a mean estimated TMRCA (adjusted for
outbreak duration) of 243 days (95\% CI 143-343), compared with
55 days (28-81) for outbreaks lacking epidemiological evidence
for an LTC (p=0.004). A threshold of 156 days predicted LTC
involvement with a sensitivity of 0.875 and a specificity of 1.We
also found 6/20 outbreaks included isolates with differing
antimicrobial susceptibility profiles, however, these had only
modestly increased pairwise diversity (mean 17.5 single
nucleotide variants (SNVs) (95\% CI 17.3-17.8) vs 12.7 SNVs
(12.5-12.8)) compared with isolates with identical antibiograms
(p<0.0001). Additionally, for 2 outbreaks, WGS identified 1 or
more isolates which were genetically distinct despite having the
outbreak PFGE pulsotype.Duration-adjusted TMRCA allowed the
involvement of LTCs in outbreaks to be identified and could be
used to decide whether screening for long-term carriage (e.g. in
healthcare workers) is warranted. Requiring identical
antibiograms to trigger investigation could miss important
contributors to outbreaks.",
journal = "J. Clin. Microbiol.",
month = may,
year = 2017,
keywords = "Staphylococcus;transmission-epidemiology;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Ankrum2017-pp,
title = "Population dynamics of \textit{Staphylococcus aureus} in Cystic
Fibrosis patients to determine transmission events utilizing
{WGS}",
author = "Ankrum, Andrea and Hall, Barry G",
abstract = "Strict infection control practices have been implemented for
healthcare visits by Cystic Fibrosis patients in an attempt to
prevent transmission of important pathogens. This study used
whole genome sequencing (WGS) to determine strain relatedness and
assess population dynamics of Staphylococcus aureus isolates from
a cohort of CF patients as assessed by strain relatedness. 311 S.
aureus isolates were collected from respiratory cultures of 115
CF patients during a 22 month study period. Whole genome
sequencing was performed and using SNP analysis, phylogenetic
trees were assembled to determine relatedness between isolates.
MRSA phenotypes were predicted using PPFS2 and compared to the
observed phenotype. The accumulation of SNPs in multiple isolates
obtained over time from the same patient was examined to
determine if a genomic molecular clock could be calculated.Pairs
of isolates with $\leq$ 71 SNP differences were considered to be
the ``same'' strain. All of the ``same'' strain isolates were
either from the same patient or siblings pairs. There were 47
examples of patients being superinfected with an unrelated
strain. Predicted MRSA phenotype was accurate in all but three
isolates. Mutation rates were unable to be determined because the
branching order in the phylogenetic tree was inconsistent with
the order of isolation.The observation that transmissions were
identified between sibling patients shows that WGS is an
effective tool for determining transmission between patients. The
observation that transmission only occurred between siblings
suggests that Staphylococcus aureus acquisition in our CF
population occurred outside the hospital environment and
indicates that current infection prevention efforts appear
effective.",
journal = "J. Clin. Microbiol.",
month = apr,
year = 2017,
keywords = "bacerial\_genetics;Staphylococcus;bacterial comparative
genomics;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Mekonnen2017-oe,
title = "Signatures of cytoplasmic proteins in the exoproteome distinguish
community- and hospital-associated methicillin-resistant
Staphylococcus aureus {USA300} lineages",
author = "Mekonnen, Solomon A and Palma Medina, Laura M and Glasner,
Corinna and Tsompanidou, Eleni and de Jong, Anne and Grasso,
Stefano and Schaffer, Marc and M{\"a}der, Ulrike and Larsen,
Anders R and Gumpert, Heidi and Westh, Henrik and V{\"o}lker, Uwe
and Otto, Andreas and Becher, D{\"o}rte and van Dijl, Jan Maarten",
abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) is the common
name for a heterogeneous group of highly drug-resistant
staphylococci. Two major MRSA classes are distinguished based on
epidemiology, namely community-associated (CA) and
hospital-associated (HA) MRSA. Notably, the distinction of CA-
and HA-MRSA based on molecular traits remains difficult due to
the high genomic plasticity of S. aureus. Here we sought to
pinpoint global distinguishing features of CA- and HA-MRSA
through a comparative genome and proteome analysis of the
notorious MRSA lineage USA300. We show for the first time that
CA- and HA-MRSA isolates can be distinguished by two distinct
extracellular protein abundance clusters that are predictive not
only for epidemiologic behavior, but also for their growth and
survival within epithelial cells. This 'exoproteome profiling'
also groups more distantly related HA-MRSA isolates into the HA
exoproteome cluster. Comparative genome analysis suggests that
these distinctive features of CA- and HA-MRSA isolates relate
predominantly to the accessory genome. Intriguingly, the
identified exoproteome clusters differ in the relative abundance
of typical cytoplasmic proteins, suggesting that signatures of
cytoplasmic proteins in the exoproteome represent a new
distinguishing feature of CA- and HA-MRSA. Our comparative genome
and proteome analysis focuses attention on potentially
distinctive roles of 'liberated' cytoplasmic proteins in the
epidemiology and intracellular survival of CA- and HA-MRSA
isolates. Such extracellular cytoplasmic proteins were recently
invoked in staphylococcal virulence, but their implication in the
epidemiology of MRSA is unprecedented.",
journal = "Virulence",
pages = "0",
month = may,
year = 2017,
keywords = "MRSA; Staphylococcus; USA300; community; epithelial cells;
exoproteome; hospital; moonlighting; protein secretion; virulence
factor;Staphylococcus;controversial;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Makarova2017-yd,
title = "Complete Genome Sequence of the {Livestock-Associated}
{Methicillin-Resistant} Strain \textit{Staphylococcus aureus}
subsp. \textit{aureus} {08S00974} (Sequence Type 398)",
author = "Makarova, Olga and Johnston, Paul and Walther, Birgit and Rolff,
Jens and Roesler, Uwe",
abstract = "We report here the complete genome sequence of the
livestock-associated methicillin-resistant Staphylococcus aureus
strain 08S00974 from sequence type 398 (ST398 LA-MRSA) isolated
from a fatting pig at a farm in Germany.",
journal = "Genome Announc.",
volume = 5,
number = 19,
month = may,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Makarova2017-tq,
title = "Complete Genome Sequence of the Disinfectant Susceptibility
Testing Reference Strain \textit{Staphylococcus aureus} subsp.
\textit{aureus} {ATCC} 6538",
author = "Makarova, Olga and Johnston, Paul and Walther, Birgit and Rolff,
Jens and Roesler, Uwe",
abstract = "We report here the complete genome sequence of the
methicillin-sensitive Staphylococcus aureus subsp. aureus strain
ATCC 6538 (FDA 209, DSM 799, WDCM 00032, and NCTC 10788).",
journal = "Genome Announc.",
volume = 5,
number = 19,
month = may,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Tewhey2012-yx,
title = "Genetic structure of community acquired methicillin-resistant
Staphylococcus aureus {USA300}",
author = "Tewhey, Ryan and Cannavino, Christopher R and Leake, John A D and
Bansal, Vikas and Topol, Eric J and Torkamani, Ali and Bradley,
John S and Schork, Nicholas J",
abstract = "BACKGROUND: Community-associated methicillin-resistant
Staphylococcus aureus (CA-MRSA) is a significant bacterial
pathogen that poses considerable clinical and public health
challenges. The majority of the CA-MRSA disease burden consists
of skin and soft tissue infections (SSTI) not associated with
significant morbidity; however, CA-MRSA also causes severe,
invasive infections resulting in significant morbidity and
mortality. The broad range of disease severity may be influenced
by bacterial genetic variation. RESULTS: We sequenced the
complete genomes of 36 CA-MRSA clinical isolates from the
predominant North American community acquired clonal type USA300
(18 SSTI and 18 severe infection-associated isolates). While all
36 isolates shared remarkable genetic similarity, we found
greater overall time-dependent sequence diversity among SSTI
isolates. In addition, pathway analysis of non-synonymous
variations revealed increased sequence diversity in the putative
virulence genes of SSTI isolates. CONCLUSIONS: Here we report the
first whole genome survey of diverse clinical isolates of the
USA300 lineage and describe the evolution of the pathogen over
time within a defined geographic area. The results demonstrate
the close relatedness of clinically independent CA-MRSA isolates,
which carry implications for understanding CA-MRSA epidemiology
and combating its spread.",
journal = "BMC Genomics",
volume = 13,
pages = "508",
month = sep,
year = 2012,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Larsen2017-ln,
title = "Emergence of livestock-associated methicillin-resistant
Staphylococcus aureus bloodstream infections in Denmark",
author = "Larsen, Jesper and Petersen, Andreas and Larsen, Anders R and
Sieber, Raphael N and Stegger, Marc and Koch, Anders and
Aarestrup, Frank M and Price, Lance B and Skov, Robert L",
abstract = "Livestock-associated methicillin-resistant Staphylococcus aureus
clonal complex 398 (LA-MRSA CC398) is causing an increasing
number of skin and soft tissue infections (SSTIs) in Denmark and
other European countries with industrial pig production. Yet, its
impact on MRSA bloodstream infections (BSIs) has not been well
studied.We investigated the clinical epidemiology of all human
cases of LA-MRSA CC398 BSI during 2010--2015. Cases of LA-MRSA
CC398 BSI were compared to cases of BSI caused by other types of
MRSA and cases of SSTI caused by LA-MRSA CC398. Whole-genome
sequence analysis was used to assess the phylogenetic
relationship among LA-MRSA CC398 isolates from Danish pigs and
cases of BSI and SSTI.The number of LA-MRSA CC398 BSIs and SSTIs
increased over the years, peaking in 2014, where LA-MRSA CC398
accounted for 16\% (7/44) and 21\% (211/985) of all MRSA BSIs and
SSTIs, corresponding to 1.2 and 37.4 cases of BSI and SSTI per
1,000,000 person-years, respectively. Most patients with LA-MRSA
CC398 BSI had no contact to livestock, although they tended to
live in rural areas. LA-MRSA CC398 caused 24.3 BSIs per 1,000
SSTIs among people with no livestock contact, which is similar to
the ratio observed for other types of MRSA. Whole-genome sequence
analysis showed that most of the BSI and SSTI isolates were
closely related to Danish pig isolates.This study demonstrates
that the increasing number of LA-MRSA CC398 BSIs occurred in
parallel with a much larger wave of LA-MRSA CC398 SSTIs and an
expanding pig reservoir.",
journal = "Clin. Infect. Dis.",
month = may,
year = 2017,
keywords = "denmark; methicillin-resistant staphylococcus aureus; skin and
soft tissue infections; animals, farm; bloodstream infection;
genome; sequence analysis; family suidae;
epidemiology;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Park2017-ym,
title = "Molecular epidemiology of Staphylococcus aureus bacteremia in a
single large Minnesota medical center in 2015 as assessed using
{MLST}, core genome {MLST} and spa typing",
author = "Park, Kyung-Hwa and Greenwood-Quaintance, Kerryl E and Uhl, James
R and Cunningham, Scott A and Chia, Nicholas and Jeraldo,
Patricio R and Sampathkumar, Priya and Nelson, Heidi and Patel,
Robin",
abstract = "Staphylococcus aureus is a leading cause of bacteremia in
hospitalized patients. Whether or not S. aureus bacteremia (SAB)
is associated with clonality, implicating potential nosocomial
transmission, has not, however, been investigated. Herein, we
examined the epidemiology of SAB using whole genome sequencing
(WGS). 152 SAB isolates collected over the course of 2015 at a
single large Minnesota medical center were studied.
Staphylococcus protein A (spa) typing was performed by PCR/Sanger
sequencing; multilocus sequence typing (MLST) and core genome
MLST (cgMLST) were determined by WGS. Forty-eight isolates (32\%)
were methicillin-resistant S. aureus (MRSA). The isolates
encompassed 66 spa types, clustered into 11 spa clonal complexes
(CCs) and 10 singleton types. 88\% of 48 MRSA isolates belonged
to spa CC-002 or -008. Methicillin-susceptible S. aureus (MSSA)
isolates were more genotypically diverse, with 61\% distributed
across four spa CCs (CC-002, CC-012, CC-008 and CC-084). By MLST,
there was 31 sequence types (STs), including 18 divided into 6
CCs and 13 singleton STs. Amongst MSSA isolates, the common MLST
clones were CC5 (23\%), CC30 (19\%), CC8 (15\%) and CC15 (11\%).
Common MRSA clones were CC5 (67\%) and CC8 (25\%); there were no
MRSA isolates in CC45 or CC30. By cgMLST analysis, there were 9
allelic differences between two isolates, with the remaining 150
isolates differing from each other by over 40 alleles. The two
isolates were retroactively epidemiologically linked by medical
record review. Overall, cgMLST analysis resulted in higher
resolution epidemiological typing than did multilocus sequence or
spa typing.",
journal = "PLoS One",
volume = 12,
number = 6,
pages = "e0179003",
month = jun,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{McClure2017-cr,
title = "Complete Genome Sequence of a {Community-Associated}
{Methicillin-Resistant} Staphylococcus aureus Hypervirulent
Strain, {USA300-C2406}, Isolated from a Patient with a Lethal
Case of Necrotizing Pneumonia",
author = "McClure, Jo-Ann and Zhang, Kunyan",
abstract = "USA300 is a predominant community-associated
methicillin-resistant Staphylococcus aureus strain causing
significant morbidity and mortality. We present here the full
annotated genome of a USA300 hypervirulent clinical strain,
USA300-C2406, isolated from a patient with a lethal case of
necrotizing pneumonia, to gain a better understanding of USA300
hypervirulence.",
journal = "Genome Announc.",
volume = 5,
number = 22,
month = jun,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Sabrina_Pankey2017-cu,
title = "Host-selected mutations converging on a global regulator drive
an adaptive leap towards symbiosis in bacteria",
author = "Sabrina Pankey, M and Foxall, Randi L and Ster, Ian M and Perry,
Lauren A and Schuster, Brian M and Donner, Rachel A and Coyle,
Matthew and Cooper, Vaughn S and Whistler, Cheryl A",
abstract = "Most bacteria that associate with animals do not cause harm, and
many are essential to health or provide other benefits. An
animal's immune system must permit these beneficial associations
and at the same time block harmful microbes. This ultimately
means that even beneficial bacteria must adapt to the immune
barriers that they encounter. Different species that live in a
close relationship with each other are known as symbionts. A
species of bacteria called Vibrio fischeri can form a mutually
beneficial symbiotic relationship with squid. The squid provide
food for the bacteria, but only the bacteria that successfully
navigate immune barriers and reach the squid's ``light organ''
are fed. In return, the bacteria produce bioluminescence, making
the nocturnal squid appear like moonlight in the water. As the
bacteria reproduce, some individuals randomly acquire genetic
mutations, some of which might improve the bacteria's chances of
survival. Which mutations and associated traits allow bacteria
to beat out the competition and evolve to become animal
symbionts? To investigate, Pankey, Foxall et al. grew V.
fischeri bacteria from several ancestors that were poor at
colonizing squid. Groups of newly hatched squid selected
potential symbionts from the resulting mix of bacteria. The
selected symbionts were allowed to reproduce within the squid to
form a new population of bacteria and were later vented out for
a new batch of squid to sort through. This was repeated to
ultimately form a final group of bacteria that had passed
through 15 squid in turn. Unexpectedly, the bacteria in the
final group all found the same solution to help them adapt to
symbiotic life with the squid: mutations to the gene that
encodes a signaling protein called BinK. Eight distinct
mutations arose that dramatically changed how the bacteria
interacted with squid. The evolved bacteria created a coating
that hid them from squid immune cells and protected them from
chemicals that squid use to kill invaders. The mutations also
altered how the bacteria communicated with each other. This
adjusted the intensity of light that they produced for their
host to a more natural level, and improved their ability to grow
on squid-provided food. Overall, the results presented by
Pankey, Foxall et al. demonstrate that small genetic mutations
can transform non-symbionts into symbionts, enabling them to
evolve rapidly to form a symbiosis with a new host. This
demonstrates that these bacteria already had the ability to
coordinate the complex behaviors necessary to overcome the
multiple barriers provided to them by the squid immune system.
Other beneficial animal--bacteria associations are likely to
work on similar principles; the study exemplifies the utility of
experimental evolution systems and lays a foundation for further
work to investigate these principles in more detail.",
journal = "eLife Sciences",
publisher = "eLife Sciences Publications Limited",
volume = 6,
pages = "e24414",
month = apr,
year = 2017,
keywords = "Vibrio fischeri; Euprymna scolopes; experimental
evolution;evolution;Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Tabuchi2017-hq,
title = "D-cycloserine increases the effectiveness of vancomycin against
vancomycin-highly resistant Staphylococcus aureus",
author = "Tabuchi, Fumiaki and Matsumoto, Yasuhiko and Ishii, Masaki and
Tatsuno, Keita and Okazaki, Mitsuhiro and Sato, Tomoaki and
Moriya, Kyoji and Sekimizu, Kazuhisa",
abstract = "Vancomycin is a widely used clinical drug to treat for infection
by methicillin-resistant Staphylococcus aureus. Some patients
show a weak response to vancomycin treatment. We previously
reported that $\beta$-lactams increase the susceptibility to
vancomycin by vancomycin-highly resistant S. aureus (VRSA)
strains obtained following repeated in vitro mutagenesis and
vancomycin selection. Here we found that the susceptibility of
the VRSA strains to vancomycin was remarkably increased by
combined treatment with D-cycloserine. On the other hand, VRSA
did not show increased susceptibility to vancomycin in
combination with bacitracin, fosfomycin, erythromycin,
lincomycin, gentamicin, levofloxacin or nisin. Furthermore, in an
in vivo infection model with silkworms, combined treatment with
vancomycin and D-cycloserine exhibited therapeutic effects,
whereas treatment with each compound alone did not. These
findings suggest that combined treatment with vancomycin and
D-cycloserine could be therapeutically effective against
infectious diseases caused by VRSA.The Journal of Antibiotics
advance online publication, 7 June 2017; doi:10.1038/ja.2017.56.",
journal = "J. Antibiot.",
month = jun,
year = 2017,
keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Ronco2017-yo,
title = "Draft Genome Sequence of a Sequence Type 398
{Methicillin-Resistant} \textit{Staphylococcus aureus} Isolate
from a Danish Dairy Cow with Mastitis",
author = "Ronco, Troels and Stegger, Marc and Pedersen, Karl",
abstract = "Livestock-associated (LA) methicillin-resistant Staphylococcus
aureus (MRSA) strains of sequence type 398 (ST398) colonize both
humans and various livestock species. In 2016, an ST398 LA-MRSA
isolate (Sa52) was collected from a Danish dairy cow with
mastitis, and here, we report the draft genome sequence of strain
Sa52.",
journal = "Genome Announc.",
volume = 5,
number = 23,
month = jun,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{McClure2017-aj,
title = "Complete Genome Sequences of Five Representative
\textit{Staphylococcus aureus} {ST398} Strains from Five Major
Sequence Heterogeneity Groups of a Diverse Isolate Collection",
author = "McClure, Jo-Ann and Zhang, Kunyan",
abstract = "Staphylococcus aureus sequence type 398 (ST398) is a rapidly
emerging livestock-associated strain causing zoonotic disease in
humans. The course of pathogen evolution remains unclear,
prompting whole-genome comparative studies in attempts to
elucidate this issue. We present the full, annotated genomes of
five newly isolated representative ST398 strains from five major
sequence heterogeneity groups of our diverse isolate collection.",
journal = "Genome Announc.",
volume = 5,
number = 23,
month = jun,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Panthee2017-vo,
title = "Draft Genome Sequence of the {Vancomycin-Resistant} Clinical
Isolate \textit{Staphylococcus aureus} {VRS3b}",
author = "Panthee, Suresh and Paudel, Atmika and Hamamoto, Hiroshi and
Sekimizu, Kazuhisa",
abstract = "We report here the draft genome sequence of the
vancomycin-resistant strain Staphylococcus aureus VRS3b. The
2.8-Mb genome, assembled into 46 contigs, harbored 2,915 putative
coding sequences. The G+C content of the genome was 32.7\%.",
journal = "Genome Announc.",
volume = 5,
number = 22,
month = jun,
year = 2017,
keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{McClure2017-aw,
title = "Complete Genome Sequence of the {Methicillin-Resistant}
\textit{Staphylococcus aureus} Colonizing Strain {M92}",
author = "McClure, Jo-Ann and Zhang, Kunyan",
abstract = "M92 is a methicillin-resistant Staphylococcus aureus (MRSA)
colonizing strain belonging to ST239-MRSA-III. It frequently
shows local nasal colonization in our hospital staff, but has
never been associated with infection. We sequenced the complete
genome of M92, in order to compare it to highly virulent MRSA
strains to gain insight into MRSA virulence factors.",
journal = "Genome Announc.",
volume = 5,
number = 23,
month = jun,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Basco2017-pi,
title = "Draft Genome Sequences of Two \textit{Staphylococcus aureus}
Strains Isolated in Succession from a Case of Bacteremia",
author = "Basco, M D S and Revollo, J R and McKinzie, P B and Agnihothram,
S and Kothari, A and Saccente, M and Hart, M E",
abstract = "Staphylococcus aureus strains MEH1 and MEH7 were successively
isolated from the blood of a patient with recurrent bacteremia.
The submitted draft genomes of strains MEH1 and MEH7 are
2,914,972 and 2,911,704 bp, respectively.",
journal = "Genome Announc.",
volume = 5,
number = 23,
month = jun,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Larsen2017-yf,
title = "Emergence of livestock-associated methicillin-resistant
Staphylococcus aureus bloodstream infections in Denmark",
author = "Larsen, Jesper and Petersen, Andreas and Larsen, Anders R and
Sieber, Raphael N and Stegger, Marc and Koch, Anders and
Aarestrup, Frank M and Price, Lance B and Skov, Robert L and
{Danish MRSA Study Group}",
abstract = "Background: Livestock-associated methicillin-resistant
Staphylococcus aureus clonal complex 398 (LA-MRSA CC398) is
causing an increasing number of skin and soft tissue infections
(SSTIs) in Denmark and other European countries with industrial
pig production. Yet, its impact on MRSA bloodstream infections
(BSIs) has not been well studied. Methods: We investigated the
clinical epidemiology of all human cases of LA-MRSA CC398 BSI
during 2010-2015. Cases of LA-MRSA CC398 BSI were compared to
cases of BSI caused by other types of MRSA and cases of SSTI
caused by LA-MRSA CC398. Whole-genome sequence analysis was used
to assess the phylogenetic relationship among LA-MRSA CC398
isolates from Danish pigs and cases of BSI and SSTI. Results: The
number of LA-MRSA CC398 BSIs and SSTIs increased over the years,
peaking in 2014, where LA-MRSA CC398 accounted for 16\% (7/44)
and 21\% (211/985) of all MRSA BSIs and SSTIs, corresponding to
1.2 and 37.4 cases of BSI and SSTI per 1,000,000 person-years,
respectively. Most patients with LA-MRSA CC398 BSI had no contact
to livestock, although they tended to live in rural areas.
LA-MRSA CC398 caused 24.3 BSIs per 1,000 SSTIs among people with
no livestock contact, which is similar to the ratio observed for
other types of MRSA. Whole-genome sequence analysis showed that
most of the BSI and SSTI isolates were closely related to Danish
pig isolates. Conclusions: This study demonstrates that the
increasing number of LA-MRSA CC398 BSIs occurred in parallel with
a much larger wave of LA-MRSA CC398 SSTIs and an expanding pig
reservoir.",
journal = "Clin. Infect. Dis.",
month = may,
year = 2017,
keywords = "MRSA; bacteremia.; humans; livestock;
zoonosis;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Larsen2017-yf,
title = "Emergence of livestock-associated methicillin-resistant
Staphylococcus aureus bloodstream infections in Denmark",
author = "Larsen, Jesper and Petersen, Andreas and Larsen, Anders R and
Sieber, Raphael N and Stegger, Marc and Koch, Anders and
Aarestrup, Frank M and Price, Lance B and Skov, Robert L and
{Danish MRSA Study Group}",
abstract = "Background: Livestock-associated methicillin-resistant
Staphylococcus aureus clonal complex 398 (LA-MRSA CC398) is
causing an increasing number of skin and soft tissue infections
(SSTIs) in Denmark and other European countries with industrial
pig production. Yet, its impact on MRSA bloodstream infections
(BSIs) has not been well studied. Methods: We investigated the
clinical epidemiology of all human cases of LA-MRSA CC398 BSI
during 2010-2015. Cases of LA-MRSA CC398 BSI were compared to
cases of BSI caused by other types of MRSA and cases of SSTI
caused by LA-MRSA CC398. Whole-genome sequence analysis was used
to assess the phylogenetic relationship among LA-MRSA CC398
isolates from Danish pigs and cases of BSI and SSTI. Results: The
number of LA-MRSA CC398 BSIs and SSTIs increased over the years,
peaking in 2014, where LA-MRSA CC398 accounted for 16\% (7/44)
and 21\% (211/985) of all MRSA BSIs and SSTIs, corresponding to
1.2 and 37.4 cases of BSI and SSTI per 1,000,000 person-years,
respectively. Most patients with LA-MRSA CC398 BSI had no contact
to livestock, although they tended to live in rural areas.
LA-MRSA CC398 caused 24.3 BSIs per 1,000 SSTIs among people with
no livestock contact, which is similar to the ratio observed for
other types of MRSA. Whole-genome sequence analysis showed that
most of the BSI and SSTI isolates were closely related to Danish
pig isolates. Conclusions: This study demonstrates that the
increasing number of LA-MRSA CC398 BSIs occurred in parallel with
a much larger wave of LA-MRSA CC398 SSTIs and an expanding pig
reservoir.",
journal = "Clin. Infect. Dis.",
month = may,
year = 2017,
keywords = "denmark; methicillin-resistant staphylococcus aureus; skin and
soft tissue infections; animals, farm; bloodstream infection;
genome; sequence analysis; family suidae;
epidemiology;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Feng2017-gr,
title = "Genome comparisons of two Taiwanese community-associated
methicillin-resistant Staphylococcus aureus {ST59} clones support
the multi-origin theory of {CA-MRSA}",
author = "Feng, Ye and Chen, Hsiu-Ling and Chen, Chih-Jung and Chen,
Chyi-Liang and Chiu, Cheng-Hsun",
abstract = "Sequence type (ST) 59 is an epidemic lineage of
community-associated methicillin-resistant Staphylococcus aureus
(CA-MRSA) in Asia. Two ST59 clones are prevalent in Taiwan: the
Taiwan clone (TW) causes severe infections, whereas the
Asian-Pacific clone (AP) is usually commensal. In this study, we
sequenced the genome and transcriptome of the representative
strains of these two clones and found their differences to focus
on three mobile genetic elements: TW carries SCCmec Type VT,
Panton-Valentine leucocidin (PVL)-encoding prophage $\Phi$Sa2,
whereas AP carries SCCmec Type IV and staphylokinase
(SAK)-encoding prophage $\Phi$Sa3. The anti-virulent role of SAK
was confirmed using murine skin and bloodstream infection models.
$\Phi$Sa3 usually integrates into the hlb gene, but in AP was
found to be integrated at the genomic island $\nu$Sa$\beta$. The
mutation of the attB site ``TGTATCCAAACTGG'' to
``TGTATCCGAATTGG'' led to a failure in the integration of
$\Phi$Sa3 in hlb, prompting atypical integration at other sites.
The sak gene possessed remarkably different patterns of
distribution among the different STs of S. aureus. We conclude
that the atypical integration of $\Phi$Sa3 may help S. aureus
adapt to the human host habitat and that the subsequent loss of
$\Phi$Sa3 contributes toward the development of a virulent
CA-MRSA lineage for wider horizontal transmission.",
journal = "Infect. Genet. Evol.",
volume = 54,
pages = "60--65",
month = jun,
year = 2017,
keywords = "Anti-virulence factor; Bacteriophage; CA-MRSA; Clone;
Staphylokinase;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Edslev2017-oi,
title = "Identification of a {PVL-negative} {SCCmec-IVa} sub-lineage of
the methicillin-resistant Staphylococcus aureus {CC80} lineage:
Understanding the clonal origin of {CA-MRSA}",
author = "Edslev, Sofie Marie and Westh, Henrik Torkil and Andersen, Paal
Skytt and Skov, Robert and Kobayashi, Nobumichi and Bartels,
Mette Damkj{\ae}r and Vandenesh, Francois and Petersen, Andreas
and Worning, Peder and Larsen, Anders Rhod and Stegger, Marc",
abstract = "OBJECTIVES: Community-acquired MRSA (CA-MRSA) isolates belonging
to clonal complex 80 (CC80) are recognized as the European
CA-MRSA. The prevailing European CA-MRSA clone carries a type IVc
staphylococcal cassette chromosome mec (SCCmec) and expresses
Panton-Valentine leukocidin (PVL). Recently, a significant
increase of PVL-negative CC80 MRSA has been observed in Denmark.
The aim of this study was to examine the genetics and the
epidemiology of these, and to compare them to the European
CA-MRSA clone in order to understand the emergence of
PVL-negative CC80 MRSA. METHODS: Phylogenetic analysis of the
CC80 S. aureus lineage was conducted from whole-genome sequences
of 217 isolates (23 MSSA and 194 MRSA) from 22 countries. All
isolates were further genetically characterized in regard to
resistance determinants and PVL carriage, and epidemiological
data was obtained for selected isolates. RESULTS: The
phylogenetic analysis revealed the existence of three distinct
clades of the CC80 lineage: i) an MSSA clade encompassing
Sub-Saharan African isolates (n=13); ii) a derived clade
encompassing the European CA-MRSA SCCmec-IVc clone (n=185); and
iii) a novel and genetically distinct clade encompassing MRSA
SCCmec-IVa isolates (n=19). All isolates in the novel clade were
PVL negative, but carried remnant parts (8 -12 kb) of the
PVL-encoding prophage $\Phi$Sa2, and were susceptible to fusidic
acid and kanamycin/amikacin. Geospatial mapping could link these
isolates to regions in the Middle East, Asia and South Pacific.
CONCLUSIONS: This study reports the emergence of a novel CC80
CA-MRSA sub-lineage, showing that the CC80 lineage is more
diverse than previously assumed.",
journal = "Clin. Microbiol. Infect.",
month = jun,
year = 2017,
keywords = "Antibiotic resistance; CA-MRSA; Epidemiology; Evolution;
Genetics; Phylogeny;
SCCmec;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Byrd2017-yt,
title = "Staphylococcus aureus and Staphylococcus epidermidis strain
diversity underlying pediatric atopic dermatitis",
author = "Byrd, Allyson L and Deming, Clay and Cassidy, Sara K B and
Harrison, Oliver J and Ng, Weng-Ian and Conlan, Sean and
Program, Nisc Comparative Sequencing and Belkaid, Yasmine and
Segre, Julia A and Kong, Heidi H",
abstract = "The heterogeneous course, severity, and treatment responses
among patients with atopic dermatitis (AD; eczema) highlight the
complexity of this multifactorial disease. Prior studies have
used traditional typing methods on cultivated isolates or
sequenced a bacterial marker gene to study the skin microbial
communities of AD patients. Shotgun metagenomic sequence
analysis provides much greater resolution, elucidating multiple
levels of microbial community assembly ranging from kingdom to
species and strain-level diversification. We analyzed microbial
temporal dynamics from a cohort of pediatric AD patients sampled
throughout the disease course. Species-level investigation of AD
flares showed greater Staphylococcus aureus predominance in
patients with more severe disease and Staphylococcus epidermidis
predominance in patients with less severe disease. At the strain
level, metagenomic sequencing analyses demonstrated clonal S.
aureus strains in more severe patients and heterogeneous S.
epidermidis strain communities in all patients. To investigate
strain-level biological effects of S. aureus, we topically
colonized mice with human strains isolated from AD patients and
controls. This cutaneous colonization model demonstrated S.
aureus strain--specific differences in eliciting skin
inflammation and immune signatures characteristic of AD
patients. Specifically, S. aureus isolates from AD patients with
more severe flares induced epidermal thickening and expansion of
cutaneous T helper 2 (TH2) and TH17 cells. Integrating
high-resolution sequencing, culturing, and animal models
demonstrated how functional differences of staphylococcal
strains may contribute to the complexity of AD disease.",
journal = "Sci. Transl. Med.",
publisher = "American Association for the Advancement of Science",
volume = 9,
number = 397,
pages = "eaal4651",
month = jul,
year = 2017,
keywords = "Staphylococcus;immunology-immunogenomics;fungus;grants;Staphylococcus\_aureus\_genome\_papers;skin\_shotgun\_microbiome",
language = "en"
}
@ARTICLE{Moradigaravand2017-mi,
title = "Evolution of the \textit{Staphylococcus argenteus} {ST2250} Clone
in Northeastern Thailand Is Linked with the Acquisition of
{Livestock-Associated} Staphylococcal Genes",
author = "Moradigaravand, Danesh and Jamrozy, Dorota and Mostowy, Rafal and
Anderson, Annaliesa and Nickerson, Emma K and Thaipadungpanit,
Janjira and Wuthiekanun, Vanaporn and Limmathurotsakul, Direk and
Tandhavanant, Sarunporn and Wikraiphat, Chanthiwa and Wongsuvan,
Gumphol and Teerawattanasook, Nittaya and Jutrakul, Yaowaruk and
Srisurat, Nuttiya and Chaimanee, Prajuab and Eoin West, T and
Blane, Beth and Parkhill, Julian and Chantratita, Narisara and
Peacock, Sharon J",
abstract = "Staphylococcus argenteus is a newly named species previously
described as a divergent lineage of Staphylococcus aureus that
has recently been shown to have a global distribution. Despite
growing evidence of the clinical importance of this species,
knowledge about its population epidemiology and genomic
architecture is limited. We used whole-genome sequencing to
evaluate and compare S. aureus (n = 251) and S. argenteus (n =
68) isolates from adults with staphylococcal sepsis at several
hospitals in northeastern Thailand between 2006 and 2013. The
majority (82\%) of the S. argenteus isolates were of multilocus
sequence type 2250 (ST2250). S. aureus was more diverse, although
43\% of the isolates belonged to ST121. Bayesian analysis
suggested an S. argenteus ST2250 substitution rate of 4.66 (95\%
confidence interval [CI], 3.12 to 6.38) mutations per genome per
year, which was comparable to the S. aureus ST121 substitution
rate of 4.07 (95\% CI, 2.61 to 5.55). S. argenteus ST2250 emerged
in Thailand an estimated 15 years ago, which contrasts with the
S. aureus ST1, ST88, and ST121 clades that emerged around 100 to
150 years ago. Comparison of S. argenteus ST2250 genomes from
Thailand and a global collection indicated a single introduction
into Thailand, followed by transmission to local and more distant
countries in Southeast Asia and further afield. S. argenteus and
S. aureus shared around half of their core gene repertoire,
indicating a high level of divergence and providing strong
support for their classification as separate species. Several
gene clusters were present in ST2250 isolates but absent from the
other S. argenteus and S. aureus study isolates. These included
multiple exotoxins and antibiotic resistance genes that have been
linked previously with livestock-associated S. aureus, consistent
with a livestock reservoir for S. argenteus These genes appeared
to be associated with plasmids and mobile genetic elements and
may have contributed to the biological success of
ST2250.IMPORTANCE In this study, we used whole-genome sequencing
to understand the genome evolution and population structure of a
systematic collection of ST2250 S. argenteus isolates. A newly
identified ancestral species of S. aureus, S. argenteus has
become increasingly known as a clinically important species that
has been reported recently across various countries. Our results
indicate that S. argenteus has spread at a relatively rapid pace
over the past 2 decades across northeastern Thailand and acquired
multiple exotoxin and antibiotic resistance genes that have been
linked previously with livestock-associated S. aureus Our
findings highlight the clinical importance and potential
pathogenicity of S. argenteus as a recently emerging pathogen.",
journal = "MBio",
volume = 8,
number = 4,
month = jul,
year = 2017,
keywords = "Staphylococcus argenteus; Staphylococcus aureus; antibiotic
resistance; genomic
epidemiology;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Weterings2017-wc,
title = "Next-generation sequence analysis reveals methicillin-resistance
transfer to a methicillin-susceptible \textit{Staphylococcus
aureus} ({MSSA}) strain that subsequently caused a
methicillin-resistant \textit{Staphylococcus aureus} ({MRSA})
outbreak: a descriptive study",
author = "Weterings, Veronica and Bosch, Thijs and Witteveen, Sandra and
Landman, Fabian and Schouls, Leo and Kluytmans, Jan",
abstract = "Resistance to methicillin in Staphylococcus aureus is primarily
caused by the mecA gene, which is carried on a mobile genetic
element: the staphylococcal cassette chromosome mec (SCCmec).
Horizontal transfer of this element is supposed to play an
important factor in the emergence of new clones of
methicillin-resistant Staphylococcus aureus (MRSA), but has been
rarely observed in real-time.In 2012, an outbreak occurred
involving a healthcare worker (HCW) and three patients all
carrying a fusidic-acid resistant MRSA strain. The husband of the
HCW was screened for MRSA carriage, but only a
methicillin-susceptible S. aureus (MSSA) was detected, which was
also resistant for fusidic acid. Multiple Locus Variable-number
Tandem Repeat Analysis (MLVA)-typing showed that both the MSSA
and the MRSA isolates were MT4053-MC0005. This finding led to the
hypothesis that the MSSA strain acquired the SCCmec and
subsequently caused an outbreak. To support this hypothesis,
next-generation sequencing of the MSSA and MRSA isolates was
performed.This study showed that the MSSA isolate clustered
closely with the outbreak isolates based on whole-genome
multilocus sequence typing (wgMLST) and the single nucleotide
polymorphism (SNP) analysis, with a distance of 17 genes and 44
SNPs, respectively. Remarkably, there were relatively large
differences in mobile genetic elements in strains within and
between individuals.The limited genetic distance between the MSSA
and the MRSA isolates in combination with a clear epidemiologic
link, support the hypothesis that the MSSA isolate acquired a
SCCmec and that the resulting MRSA strain caused an
outbreak.IMPORTANCE This report shows that acquisition of the
staphylococcal cassette chromosome mec (SCCmec) by a
methicillin-susceptible S. aureus does occur. In this case it
concerned a healthcare worker (HCW) and this subsequently caused
an outbreak in a vulnerable group of patients. The whole genome
sequence based analysis further showed that considerable genetic
variability occurred in a relatively short time span. These
findings are important to reconsider the exclusion of HCW with
regard to control measures for methicillin-resistant S. aureus
Also the genetic variation in related microorganisms is likely to
be larger than currently assumed.",
journal = "J. Clin. Microbiol.",
month = jul,
year = 2017,
keywords = "Staphylococcus;antibiotics;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{DeFrancesco2017-dv,
title = "Genome-wide screen for genes involved in {eDNA} release during
biofilm formation by \textit{Staphylococcus aureus}",
author = "DeFrancesco, Alicia S and Masloboeva, Nadezda and Syed, Adnan K
and DeLoughery, Aaron and Bradshaw, Niels and Li, Gene-Wei and
Gilmore, Michael S and Walker, Suzanne and Losick, Richard",
abstract = "Staphylococcus aureus is a leading cause of both nosocomial and
community-acquired infection. Biofilm formation at the site of
infection reduces antimicrobial susceptibility and can lead to
chronic infection. During biofilm formation, a subset of cells
liberate cytoplasmic proteins and DNA, which are repurposed to
form the extracellular matrix that binds the remaining cells
together in large clusters. Using a strain that forms robust
biofilms in vitro during growth under glucose supplementation, we
carried out a genome-wide screen for genes involved in the
release of extracellular DNA (eDNA). A high-density transposon
insertion library was grown under biofilm-inducing conditions,
and the relative frequency of insertions was compared between
genomic DNA (gDNA) collected from cells in the biofilm and eDNA
from the matrix. Transposon insertions into genes encoding
functions necessary for eDNA release were identified by reduced
representation in the eDNA. On direct testing, mutants of some of
these genes exhibited markedly reduced levels of eDNA and a
concomitant reduction in cell clustering. Among the genes with
robust mutant phenotypes were gdpP, which encodes a
phosphodiesterase that degrades the second messenger
cyclic-di-AMP, and xdrA, the gene for a transcription factor
that, as revealed by RNA-sequencing analysis, influences the
expression of multiple genes, including many involved in cell
wall homeostasis. Finally, we report that growth in
biofilm-inducing medium lowers cyclic-di-AMP levels and does so
in a manner that depends on the gdpP phosphodiesterase gene.",
journal = "Proc. Natl. Acad. Sci. U. S. A.",
month = jul,
year = 2017,
keywords = "Staphylococcus aureus; biofilm; cyclic-di-AMP;
eDNA;Staphylococcus;tn-seq;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Putonti2017-qz,
title = "Draft Genome Sequences of Two {ATCC} \textit{Staphylococcus
aureus} subsp. \textit{aureus} Strains",
author = "Putonti, Catherine and Kalesinskas, Laurynas and Cudone, Evan and
Engelbrecht, Kathleen C and Koenig, David W and Wolfe, Alan J",
abstract = "Draft genome sequences for Staphylococcus aureus subsp. aureus
Rosenbach ATCC 14458 and ATCC 27217 strains were investigated.
The genome sizes were 2,880,761 bp and 2,759,100 bp,
respectively. Strain ATCC 14458 was assembled into 39 contigs,
including 3 plasmids, and strain ATCC 27217 was assembled into 25
contigs, including 2 plasmids.",
journal = "Genome Announc.",
volume = 5,
number = 27,
month = jul,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Sahibzada2017-gl,
title = "Transmission of highly virulent community-associated {MRSA}
{ST93} and livestock-associated {MRSA} {ST398} between humans and
pigs in Australia",
author = "Sahibzada, S and Abraham, S and Coombs, G W and Pang, S and
Hern{\'a}ndez-Jover, M and Jordan, D and Heller, J",
abstract = "Pigs have been recognised as a reservoir of livestock associated
methicillin-resistant Staphylococcus aureus (LA-MRSA) in Europe,
Asia and North America. However, little is known about the
presence and distribution of MRSA in the Australian pig
population and pig industry. This study describes the presence,
distribution and molecular characteristics of the human adapted
Australian CA-MRSA ST93 isolated from pigs, people, and the
environment within a piggery. Isolates were subjected to
antibiotic susceptibility testing, DNA microarray, whole genome
sequencing, multi locus sequence typing, virulence and resistance
gene characterization and phylogenetic analysis. MRSA were
isolated from 60\% (n = 52) of farm workers where 84\% of
isolates returned ST93 and the rest ST398. Of the thirty-one pig
isolates tested further, an equal number of ST398 and ST93 (15
each) and one as ST30-V were identified. Four of six
environmental isolates were identified as ST93 and two as ST398.
This study has identified for the first time in Australia the
occurrence of CA-MRSA ST93 and LA-MRSA ST398 amongst farm
workers, pigs, and the farm environment. Comparative genome
analysis indicates that ST398 is likely to have been introduced
into Australia from Europe or North America. This study also
reports the first linezolid resistant MRSA isolated in Australia.",
journal = "Sci. Rep.",
volume = 7,
number = 1,
pages = "5273",
month = jul,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Ward2016-el,
title = "Identification of source and sink populations for the emergence
and global spread of the {East-Asia} clone of
community-associated {MRSA}",
author = "Ward, Melissa J and Goncheva, Mariya and Richardson, Emily and
McAdam, Paul R and Raftis, Emma and Kearns, Angela and Daum,
Robert S and David, Michael Z and Lauderdale, Tsai Ling and
Edwards, Giles F and Nimmo, Graeme R and Coombs, Geoffrey W and
Huijsdens, Xander and Woolhouse, Mark E J and Fitzgerald, J Ross",
abstract = "BACKGROUND: Our understanding of the factors influencing the
emergence, dissemination and global distribution of epidemic
clones of bacteria is limited. ST59 is a major epidemic clone of
community-associated MRSA in East Asia, responsible for extensive
morbidity and mortality, but has a much lower prevalence in other
parts of the world. The geographic origin of ST59 and its
international routes of dissemination are unclear and disputed in
the literature. RESULTS: To investigate the origin and spread of
the ST59 clone, we obtained whole genome sequences of isolates
from four continents, sampled over more than a decade, and
carried out a time-scaled phylogeographic analysis. We discover
that two distinct ST59 clades emerged concurrently, in East Asia
and the USA, but underwent clonal expansion at different times.
The East Asia clade was strongly enriched for gene determinants
associated with antibiotic resistance, consistent with regional
differences in antibiotic usage. Both clones spread independently
to Australia and Europe, and we found evidence of the persistence
of multi-drug resistance following export from East Asia. Direct
transfer of strains between Taiwan and the USA was not observed
in either direction, consistent with geographic niche exclusion.
CONCLUSIONS: Our results resolve a longstanding controversy
regarding the origin of the ST59 clone, revealing the major
global source and sink populations and routes for the spread of
multi-drug resistant clones. Additionally, our findings indicate
that diversification of the accessory genome of epidemic clones
partly reflects region-specific patterns of antibiotic usage,
which may influence bacterial fitness after transmission to
different geographic locations.",
journal = "Genome Biol.",
volume = 17,
number = 1,
pages = "160",
month = jul,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Hayden2016-uc,
title = "Chlorhexidine and Mupirocin Susceptibility of
{Methicillin-Resistant} Staphylococcus aureus Isolates in the
{REDUCE-MRSA} Trial",
author = "Hayden, Mary K and Lolans, Karen and Haffenreffer, Katherine and
Avery, Taliser R and Kleinman, Ken and Li, Haiying and Kaganov,
Rebecca E and Lankiewicz, Julie and Moody, Julia and Septimus,
Edward and Weinstein, Robert A and Hickok, Jason and Jernigan,
John and Perlin, Jonathan B and Platt, Richard and Huang, Susan S",
abstract = "Whether targeted or universal decolonization strategies for the
control of methicillin-resistant Staphylococcus aureus (MRSA)
select for resistance to decolonizing agents is unresolved. The
REDUCE-MRSA trial (ClinicalTrials registration no. NCT00980980)
provided an opportunity to investigate this question. REDUCE-MRSA
was a 3-arm, cluster-randomized trial of either screening and
isolation without decolonization, targeted decolonization with
chlorhexidine and mupirocin, or universal decolonization without
screening to prevent MRSA infection in intensive-care unit (ICU)
patients. Isolates from the baseline and intervention periods
were collected and tested for susceptibility to chlorhexidine
gluconate (CHG) by microtiter dilution; mupirocin susceptibility
was tested by Etest. The presence of the qacA or qacB gene was
determined by PCR and DNA sequence analysis. A total of 3,173
isolates were analyzed; 2 were nonsusceptible to CHG (MICs, 8
$\mu$g/ml), and 5/814 (0.6\%) carried qacA or qacB At baseline,
7.1\% of MRSA isolates expressed low-level mupirocin resistance,
and 7.5\% expressed high-level mupirocin resistance. In a
mixed-effects generalized logistic regression model, the odds of
mupirocin resistance among clinical MRSA isolates or MRSA
isolates acquired in an ICU in intervention versus baseline
periods did not differ across arms, although estimates were
imprecise due to small numbers. Reduced susceptibility to
chlorhexidine and carriage of qacA or qacB were rare among MRSA
isolates in the REDUCE-MRSA trial. The odds of mupirocin
resistance were no different in the intervention versus baseline
periods across arms, but the confidence limits were broad, and
the results should be interpreted with caution.",
journal = "J. Clin. Microbiol.",
volume = 54,
number = 11,
pages = "2735--2742",
month = nov,
year = 2016,
keywords = "Staphylococcus;chlorhexidine;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Sun2017-ib,
title = "Characterization of a {PVL-negative} community-acquired
methicillin-resistant Staphylococcus aureus strain of sequence
type 88 in China",
author = "Sun, Lu and Wu, Dandan and Chen, Yan and Wang, Qian and Wang,
Haiping and Yu, Yunsong",
abstract = "Sequence type 88 community-acquired methicillin-resistant
Staphylococcus aureus (CA-MRSA) strain SR434, isolated from an
outpatient with skin and soft tissue infection, was subjected to
whole genome sequencing, antimicrobial susceptibility testing,
mouse skin infection model and hemolysis analysis to identify its
virulence and resistance determinants. MRSA strain SR434 is
resistant to clindamycin, erythromycin and fosfomycin. Four
plasmids with resistance genes were identified in this strain,
including a 20,658bp blaZ-carrying plasmid, a 2473bp
ermC-carrying plasmid, a 2622bp fosB7-carrying plasmid (86\%
identity with plasmid in a ST2590 MRSA strain) and a 4817bp
lnuA-carrying plasmid (99\% identity with pLNU4 from bovine
coagulase-nagetive Staphylococci). This strain contains
staphylococcal cassette chromosome mec type IV and does not
contain arginine catabolic mobile element or
Panton-Valentine-Leukocidin. SR434 harbors genomic islands
$\nu$Sa$\alpha$, $\nu$Sa$\beta$, $\nu$Sa$\gamma$ and $\Phi$Sa3
and pathogenicity islands $\nu$Sa2 that carries genes encoding
toxic shock syndrome toxin 1, superantigen enterotoxin C and
superantigen enterotoxin L. Mouse skin infection model results
show that SR434 had similar virulence potential causing invasive
skin infection as a PVL-negative epidemic Korea clone HL1 (ST72).
CA-MRSA strain of ST88 lineage might be a great concern for its
high virulence. PVL has limited contribution to virulence
phenotype among this lineage.",
journal = "Int. J. Med. Microbiol.",
month = jul,
year = 2017,
keywords = "CA-MRSA; Genome; High virulence;
ST88;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Harkins2017-uw,
title = "Methicillin-resistant Staphylococcus aureus emerged long before
the introduction of methicillin into clinical practice",
author = "Harkins, Catriona P and Pichon, Bruno and Doumith, Michel and
Parkhill, Julian and Westh, Henrik and Tomasz, Alexander and de
Lencastre, Herminia and Bentley, Stephen D and Kearns, Angela M
and Holden, Matthew T G",
abstract = "BACKGROUND: The spread of drug-resistant bacterial pathogens
poses a major threat to global health. It is widely recognised
that the widespread use of antibiotics has generated selective
pressures that have driven the emergence of resistant strains.
Methicillin-resistant Staphylococcus aureus (MRSA) was first
observed in 1960, less than one year after the introduction of
this second generation beta-lactam antibiotic into clinical
practice. Epidemiological evidence has always suggested that
resistance arose around this period, when the mecA gene encoding
methicillin resistance carried on an SCCmec element, was
horizontally transferred to an intrinsically sensitive strain of
S. aureus. RESULTS: Whole genome sequencing a collection of the
first MRSA isolates allows us to reconstruct the evolutionary
history of the archetypal MRSA. We apply Bayesian phylogenetic
reconstruction to infer the time point at which this early MRSA
lineage arose and when SCCmec was acquired. MRSA emerged in the
mid-1940s, following the acquisition of an ancestral type I
SCCmec element, some 14 years before the first therapeutic use of
methicillin. CONCLUSIONS: Methicillin use was not the original
driving factor in the evolution of MRSA as previously thought.
Rather it was the widespread use of first generation beta-lactams
such as penicillin in the years prior to the introduction of
methicillin, which selected for S. aureus strains carrying the
mecA determinant. Crucially this highlights how new drugs,
introduced to circumvent known resistance mechanisms, can be
rendered ineffective by unrecognised adaptations in the bacterial
population due to the historic selective landscape created by the
widespread use of other antibiotics.",
journal = "Genome Biol.",
volume = 18,
number = 1,
pages = "130",
month = jul,
year = 2017,
keywords = "Antibiotic resistance; MRSA; Staphylococcus
aureus;Staphylococcus;antibiotics;transmission-epidemiology;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Arias2017-iu,
title = "Molecular Epidemiology and Phylogenomics of
\textit{Staphylococcus aureus} Bacteremia in {Latin-America}: A
Prospective Cohort Multicenter Study in Nine Countries",
author = "Arias, Cesar A and Reyes, Jinnethe and Carvajal, Lina Paola and
Rincon, Sandra and Diaz, Lorena and Panesso, Diana and Ibarra,
Gabriel and Rios, Rafael and Munita, Jose M and Salles, Mauro J
and Alvarez-Moreno, Carlos and Labarca, Jaime and Garcia,
Coralith and Luna, Carlos M and Mejia-Villatoro, Carlos and
Zurita, Jeannete and Guzman-Blanco, Manuel and Rodriguez-Noriega,
Eduardo and Narechania, Apurva and Rojas, Laura J and Planet,
Paul J and Weinstock, George M and Gotuzzo, Eduardo and Seas,
Carlos",
abstract = "Staphylococcus aureus are important pathogens causing a spectrum
of diseases ranging from mild skin and soft tissue infections to
life-threatening conditions. Bloodstream infections are
particularly important and the treatment approach is complicated
by the presence of methicillin resistance among S. aureus
isolates (MRSA). Emergence of new genetic lineages of MRSA has
occurred in Latin America (LA) with the rise and dissemination of
the community-associated USA300 Latin American Variant
(USA300-LV). Here, we prospectively characterized bloodstream
MRSA recovered from selected hospitals in 9 Latin American
countries. All isolates were typed by pulsed field gel
electrophoresis (PFGE) and subjected to antibiotic susceptibility
testing. Whole genome sequencing was performed in 96 MRSA
representatives. MRSA represented 45\% of all isolates (out of
1,185 S. aureus). The majority of MRSA isolates belonged to
clonal cluster (CC) 5. In Colombia and Ecuador, most isolates
($\geq$ 72\%) belonged to the USA300-LV lineage (CC8).
Phylogenetic reconstructions indicated that MRSA isolates from
participating hospitals belonged to three major clades. Clade A
grouped isolates with ST5, ST105, and ST1011 (mostly SCCmec I and
II). Clade B included ST8, ST88, ST97, and ST72 strains (SCCmec
IV, subtypes a, b, and c/E) and clade C grouped mostly
Argentinian MRSA belonging to ST30. In summary, CC5 MRSA was
prevalent in bloodstream infections in LA with the exception of
Colombia and Ecuador where USA300-LV is now the dominant lineage.
Clonal replacement appears to be a common phenomenon and
continuous surveillance is crucial to identify changes in the
molecular epidemiology of MRSA.",
journal = "Antimicrob. Agents Chemother.",
month = jul,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Hung2016-fz,
title = "Molecular Evolutionary Pathways toward Two Successful
{Community-Associated} but {Multidrug-Resistant} {ST59}
{Methicillin-Resistant} Staphylococcus aureus Lineages in Taiwan:
Dynamic Modes of Mobile Genetic Element Salvages",
author = "Hung, Wei-Chun and Wan, Tsai-Wen and Kuo, Yu-Chia and Yamamoto,
Tatsuo and Tsai, Jui-Chang and Lin, Yu-Tzu and Hsueh, Po-Ren and
Teng, Lee-Jene",
abstract = "Clonal complex 59 (CC59) Staphylococcus aureus in Taiwan includes
both methicillin-susceptible S. aureus (MSSA) and
methicillin-resistant S. aureus (MRSA). As the most prominent
community-associated MRSA (CA-MRSA) in Taiwan, CC59 has two major
clones characterized as PVL-negative SCCmec IV (carrying the
staphylococcal cassette chromosome mec IV but Panton-Valentine
leukocidin-negative) and PVL-positive SCCmec V (5C2\&5). We
investigated the drug resistance, phylogeny and the distribution
and sequence variation of SCCmec, staphylococcal bacteriophage
$\varphi$SA3, genomic island $\nu$Sa$\beta$ and MES (an
enterococcal mobile genetic element conferring multidrug
resistance) in 195 CC59 S. aureus. Sequencing and PCR mapping
revealed that all of the CC59/SCCmec V (5C2\&5) MRSA strains had
acquired MESPM1 or its segregants, and obtained a
$\varphi$SA3-related fragment in $\nu$Sa$\beta$. In contrast,
MES6272-2 and MES4578, which showed gentamicin resistance that
was not encoded by MESPM1, were dominant in SCCmec IVg MRSA.
Translocation of a whole $\varphi$SA3 into $\nu$Sa$\beta$ instead
of only a $\varphi$SA3-related fragment was common in SCCmec IVg
MRSA. However, the non-subtype-g SCCmec IV MRSA (SCCmec IVa is
the major) still carried MES and $\nu$Sa$\beta$ structures
similar to those in SCCmec V (5C2\&5) MRSA. A minimum spanning
tree constructed by multiple-locus variable-number tandem repeat
analysis revealed that SCCmec IVg MRSA and SCCmec V (5C2\&5) MRSA
grouped respectively in two major clades. The CC59 MSSA was
equally distributed among the two clades, while the non-subtype-g
SCCmec IV MRSA mostly clustered with SCCmec V (5C2\&5) MRSA. Our
findings strongly suggest that CC59 MSSA acquired divergent
mobile genetic elements and evolved to SCCmec IVg MRSA and SCCmec
V (5C2\&5) MRSA/non-subtype-g SCCmec IV MRSA independently. The
evolutionary history of CC59 S. aureus explains how mobile
genetic elements increase the antimicrobial resistance and
virulence and contribute to the success of CA-MRSA in Taiwan.",
journal = "PLoS One",
volume = 11,
number = 9,
pages = "e0162526",
month = sep,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Werth2017-wu,
title = "Emergence of dalbavancin non-susceptible, vancomycin-intermediate
Staphylococcus aureus ({VISA}) after treatment of {MRSA} central
line-associated bloodstream infection with a dalbavancin- and
vancomycin-containing regimen",
author = "Werth, Brian J and Jain, Rupali and Hahn, Andrew and Cummings,
Lisa and Weaver, Tatiana and Waalkes, Adam and Sengupta, Dhruba
and Salipante, Stephen J and Rakita, Robert M and Butler-Wu,
Susan M",
abstract = "OBJECTIVES: Dalbavancin is a long-acting lipoglycopeptide with
activity against Gram-positives, including methicillin-resistant
Staphylococcus aureus(MRSA). The potential for lipoglycopeptides,
with half-lives greater than one-week, to select for resistance
is unknown. Here we explore a case of MRSA central
line-associated blood stream infection in which dalbavancin and
vancomycin non-susceptibility emerged in a urine isolate
collected after the patient was treated with vancomycin and
dalbavancin sequentially. METHODS: Isolates from blood and urine
underwent susceptibility testing, and whole genome sequencing
(WGS). The blood isolate was subjected to successive passage in
vitro in the presence of escalating dalbavancin concentrations
and the emergent isolate was subjected to repeat susceptibility
testing and WGS. RESULTS: The blood isolate was fully susceptible
to vancomycin, however, MICs of the urine isolate to dalbavancin,
vancomycin, telavancin and daptomycin were $\geq$4-fold higher
than the blood-derived strain. Both strains were
indistinguishable by spa and variable number tandem repeat (VNTR)
typing, and WGS revealed only 7 variants, indicating clonality.
Four variants affected genes, including a non-synonymous change
in yvqF, which has been implicated in glycopeptide resistance.
Vancomycin and dalbavancin non-susceptibility emerged in the
blood isolate after successive passage in vitro in the presence
of dalbavancin, and WGS identified a single non-synonymous
variant in yvqF. CONCLUSIONS: This is the first case in which
VISA has emerged in the context of a dalbavancin-containing
regimen. The selection for cross-resistance to vancomycin in
vitro by dalbavancin exposure alone is troubling. Clinicians
should be aware of the possibility for emergence of dalbavancin
non-susceptibility and glycopeptide cross-resistance arising
following therapy.",
journal = "Clin. Microbiol. Infect.",
month = aug,
year = 2017,
keywords = "CLABSI; cross-resistance; glycopeptide resistance;
lipoglycopeptide;Staphylococcus;confirmed\_SA-resistance-mutation;Papers\_for\_Michelle;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Hau2017-ag,
title = "Complete Genome Sequence of {Livestock-Associated}
{Methicillin-Resistant} \textit{Staphylococcus aureus} Sequence
Type 398 Isolated from Swine in the United States",
author = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and Frana,
Timothy S and Nicholson, Tracy L",
abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) colonizes and
causes disease in many animal species. Livestock-associated MRSA
(LA-MRSA) isolates are represented by isolates of the sequence
type 398 (ST398). These isolates are considered to be livestock
adapted. This report provides the complete genome sequence of one
swine-associated LA-MRSA ST398 isolate from the United States.",
journal = "Genome Announc.",
volume = 5,
number = 32,
month = aug,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Hau2017-vj,
title = "Complete Genome Sequence of a {Livestock-Associated}
{Methicillin-Resistant} \textit{Staphylococcus aureus} Sequence
Type 5 Isolate from the United States",
author = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and Frana,
Timothy S and Nicholson, Tracy L",
abstract = "Livestock-associated methicillin-resistant Staphylococcus aureus
(LA-MRSA) may be the largest MRSA reservoir outside the hospital
setting. One concern with LA-MRSA is the acquisition of novel
mobile genetic elements by these isolates. Here, we report the
complete genome sequence of a swine LA-MRSA sequence type 5
isolate from the United States.",
journal = "Genome Announc.",
volume = 5,
number = 32,
month = aug,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Harrison2017-fy,
title = "Genomic surveillance reveals low prevalence of
livestock-associated methicillin-resistant Staphylococcus aureus
in the East of England",
author = "Harrison, Ewan M and Coll, Francesc and Toleman, Michelle S and
Blane, Beth and Brown, Nicholas M and T{\"o}r{\"o}k, M Estee and
Parkhill, Julian and Peacock, Sharon J",
abstract = "Livestock-associated methicillin-resistant Staphylococcus aureus
(LA-MRSA) is an emerging problem in many parts of the world.
LA-MRSA has been isolated previously from animals and humans in
the United Kingdom (UK), but the prevalence is unknown. The aim
of this study was to determine the prevalence and to describe the
molecular epidemiology of LA-MRSA isolated in the East of England
(broadly Cambridge and the surrounding area). We accessed whole
genome sequence data for 2,283 MRSA isolates from 1,465 people
identified during a 12-month prospective study between 2012 and
2013 conducted in the East of England, United Kingdom. This
laboratory serves four hospitals and 75 general practices. We
screened the collection for multilocus sequence types (STs) and
for host specific resistance and virulence factors previously
associated with LA-MRSA. We identified 13 putative LA-MRSA
isolates from 12 individuals, giving an estimated prevalence of
0.82\% (95\% CI 0.47\% to 1.43\%). Twelve isolates were mecC-MRSA
(ten CC130, one ST425 and one ST1943) and single isolate was
ST398. Our data demonstrate a low burden of LA-MRSA in the East
of England, but the detection of mecC-MRSA and ST398 indicates
the need for vigilance. Genomic surveillance provides a mechanism
to detect and track the emergence and spread of MRSA clones of
human importance.",
journal = "Sci. Rep.",
volume = 7,
number = 1,
pages = "7406",
month = aug,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Caldelari2017-tn,
title = "Complete Genome Sequence and Annotation of the
\textit{Staphylococcus aureus} Strain {HG001}",
author = "Caldelari, Isabelle and Chane-Woon-Ming, B{\'e}atrice and Noirot,
C{\'e}line and Moreau, Karen and Romby, Pascale and Gaspin,
Christine and Marzi, Stefano",
abstract = "Staphylococcus aureus is an opportunistic Gram-positive pathogen
responsible for a wide range of infections from minor skin
abscesses to life-threatening diseases. Here, we report the draft
genome assembly and current annotation of the HG001 strain, a
derivative of the RN1 (NCT8325) strain with restored rbsU (a
positive activator of SigB).",
journal = "Genome Announc.",
volume = 5,
number = 32,
month = aug,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Grinberg2017-ax,
title = "Genomic epidemiology of methicillin-susceptible Staphylococcus
aureus across colonisation and skin and soft tissue infection",
author = "Grinberg, Alex and Biggs, Patrick J and Zhang, Ji and Ritchie,
Stephen and Oneroa, Zachary and O'Neil, Charlotte and Karkaba,
Ali and Velathanthiri, Niluka S and Coombs, Geoffrey W",
abstract = "OBJECTIVES: Staphylococcus aureus skin and soft tissue infection
(Sa-SSTI) places a significant burden on healthcare systems. New
Zealand has a high incidence of Sa-SSTI, and here most morbidity
is caused by a polyclonal methicillin-susceptible (MSSA)
population. However, MSSA also colonise asymptomatically the
cornified epithelia of approximately 20\% of the population, and
their divide between commensalism and pathogenicity is poorly
understood. We aimed to see whether MSSA is genetically
differentiated across asymptomatic colonisation and SSTI; and
given the close interactions between people and pets, whether
strains isolated from pets differ from human strains. METHODS: We
compared the genomes of contemporaneous asymptomatic colonisation
and clinical MSSA isolates obtained in New Zealand from humans
and pets. RESULTS: Core and accessory genome comparisons revealed
a homogeneous bacterial population across colonisation, disease,
humans, and pets. The rate of MSSA colonisation in dogs was
comparatively low (5.4\%). CONCLUSIONS: In New Zealand, most
Sa-SSTI morbidity is caused by a random sample of the colonising
MSSA population, consistent with the opportunistic infection
paradigm rather than a model distinguishing pathogenic from
innocuous strains. Thus, studies of host factors determining
colonisation and immune-escape may be more beneficial than
comparative virulence studies. Contact with house-hold pets may
pose low zoonotic risk.",
journal = "J. Infect.",
month = aug,
year = 2017,
keywords = "SSTI; Skin and soft tissue infection; Staphylococcus aureus;
Whole genome sequencing;
Zoonoses;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Recker2017-lp,
title = "Clonal differences in Staphylococcus aureus
bacteraemia-associated mortality",
author = "Recker, Mario and Laabei, Maisem and Toleman, Michelle S and
Reuter, Sandra and Saunderson, Rebecca B and Blane, Beth and
T{\"o}r{\"o}k, M Estee and Ouadi, Khadija and Stevens, Emily and
Yokoyama, Maho and Steventon, Joseph and Thompson, Luke and
Milne, Gregory and Bayliss, Sion and Bacon, Leann and Peacock,
Sharon J and Massey, Ruth C",
abstract = "The bacterium Staphylococcus aureus is a major human pathogen for
which the emergence of antibiotic resistance is a global public
health concern. Infection severity, and in particular
bacteraemia-associated mortality, has been attributed to several
host-related factors, such as age and the presence of
comorbidities. The role of the bacterium in infection severity is
less well understood, as it is complicated by the multifaceted
nature of bacterial virulence, which has so far prevented a
robust mapping between genotype, phenotype and infection outcome.
To investigate the role of bacterial factors in contributing to
bacteraemia-associated mortality, we phenotyped a collection of
sequenced clinical S. aureus isolates from patients with
bloodstream infections, representing two globally important
clonal types, CC22 and CC30. By adopting a genome-wide
association study approach we identified and functionally
verified several genetic loci that affect the expression of
cytolytic toxicity and biofilm formation. By analysing the pooled
data comprising bacterial genotype and phenotype together with
clinical metadata within a machine-learning framework, we found
significant clonal differences in the determinants most
predictive of poor infection outcome. Whereas elevated cytolytic
toxicity in combination with low levels of biofilm formation was
predictive of an increased risk of mortality in infections by
strains of a CC22 background, these virulence-specific factors
had little influence on mortality rates associated with CC30
infections. Our results therefore suggest that different clones
may have adopted different strategies to overcome host responses
and cause severe pathology. Our study further demonstrates the
use of a combined genomics and data analytic approach to enhance
our understanding of bacterial pathogenesis at the individual
level, which will be an important step towards personalized
medicine and infectious disease management.A genome-wide
association approach identifies differential biofilm and
virulence attributes associated with mortality in two
Staphylococcus aureus clonal complexes.",
journal = "Nat Microbiol",
month = aug,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Kleinert2017-cf,
title = "Influence of {IS\textit{256}} on genome variability and formation
of {SCV} in \textit{Staphylococcus aureus}",
author = "Kleinert, Franziska and Kallies, Ren{\'e} and Hort, Michael and
Zweynert, Annegret and Szekat, Christiane and Nagel, Michael and
Bierbaum, Gabriele",
abstract = "Staphylococcus aureus has acquired resistance to nearly all
antibiotics used in clinical practice. Whereas some resistance
mechanisms are conferred by uptake of resistance genes, others
evolve by mutation. Here, the insertion sequence 256 (IS256) has
been shown to play a role, e. g. in S. aureus strains displaying
intermediate resistance to vancomycin (VISA).To characterize the
IS256 insertion sites in the genomes of two closely related
sequence type (ST) 247 VISA strains, all insertions were mapped
in both VISA and a susceptible control strain. The results showed
that the three ST247 strains contained the highest number so far
of IS256 insertions of all sequenced S. aureus strains.
Furthermore, in contrast to the other IS elements in these
genomes, the IS256 insertion sites were not identical in the
closely related strains, indicating a high transposition
frequency of IS256 When IS256 was introduced into a laboratory
strain which was then cultured in the presence of antibiotics, it
was possible to isolate small colony variants (SCV) that
possessed IS256 insertions in guaA and hemY that displayed
increased resistance to vancomycin and aminoglycosides,
respectively. For these clones, a very rapid reversion to the
wild type was observed, that resembled the fast reversion of
clinical SCV. The reversion was caused by excision of IS256 in a
small number of fast growing clones that quickly outcompeted the
SCVs in broth cultures. In conclusion, the presence of IS256
confers a strong genomic plasticity that is useful for adaptation
to antibiotic stress.",
journal = "Antimicrob. Agents Chemother.",
month = jun,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Panthee2017-to,
title = "Genomic analysis of vancomycin-resistant Staphylococcus aureus
{VRS3b} and its comparison with other {VRSA} isolates",
author = "Panthee, Suresh and Hamamoto, Hiroshi and Paudel, Atmika and
Sekimizu, Kazuhisa",
abstract = "High-level vancomycin resistance among Staphylococcus aureus
poses a grave threat to global health as the treatment options
for this pathogen are very limited. A detailed evaluation of the
genetic background of vancomycin-resistant S. aureus (VRSA) is
expected to facilitate the understanding of its origin and
pathogenicity. In this study, we performed the genetic analysis
of the clinical VRSA isolates and identified the genetic basis of
resistance to multiple antibiotics among these strains, based on
the available draft genome sequences. In addition, we generated
the draft genome of the strain VRS3b, which was considered to be
same as VRS3a based on its isolation from the same patient. We
found that strain VRS3b did not harbor the genes responsible for
tetracycline and gentamicin, which was further confirmed by the
sensitivity towards these antibiotics. Our results suggest that
the strains VRS3a and VRS3b are different from the view of
antibiotic resistance and highlight the possibility of generation
of two distinct VRSA strains from the same patient.",
journal = "Drug Discov. Ther.",
month = apr,
year = 2017,
keywords = "Staphylococcus aureus; genomics; methicillin; resistance;
vancomycin;Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Chow2017-ed,
title = "{MRSA} Transmission Dynamics Among Interconnected Acute,
{Intermediate-Term}, and {Long-Term} Healthcare Facilities in
Singapore",
author = "Chow, Angela and Lim, Vanessa W and Khan, Ateeb and Pettigrew,
Kerry and Lye, David C B and Kanagasabai, Kala and Phua, Kelvin
and Krishnan, Prabha and Ang, Brenda and Marimuthu, Kalisvar and
Hon, Pei-Yun and Koh, Jocelyn and Leong, Ian and Parkhill, Julian
and Hsu, Li-Yang and Holden, Matthew T G",
abstract = "Background: Methicillin-resistant Staphylococcus aureus (MRSA) is
the most common healthcare-associated multidrug-resistant
organism. Despite the interconnectedness between acute care
hospitals (ACHs) and intermediate- and long-term care facilities
(ILTCFs), the transmission dynamics of MRSA between healthcare
settings is not well understood. Methods: We conducted a
cross-sectional study in a network comprising an ACH and 5
closely affiliated ILTCFs in Singapore. A total of 1700
inpatients were screened for MRSA over a 6-week period in 2014.
MRSA isolates underwent whole-genome sequencing, with a pairwise
single-nucleotide polymorphism (Hamming distance) cutoff of 60
core genome single-nucleotide polymorphisms used to define recent
transmission clusters (clades) for the 3 major clones. Results:
MRSA prevalence was significantly higher in intermediate-term
(29.9\%) and long-term (20.4\%) care facilities than in the ACH
(11.8\%) (P < .001). The predominant clones were sequence type
[ST] 22 (n = 183; 47.8\%), ST45 (n = 129; 33.7\%), and ST239 (n =
26; 6.8\%), with greater diversity of STs in ILTCFs relative to
the ACH. A large proportion of the clades in ST22 (14 of 21
clades; 67\%) and ST45 (7 of 13; 54\%) included inpatients from
the ACH and ILTCFs. The most frequent source of the interfacility
transmissions was the ACH (n = 28 transmission events; 36.4\%).
Conclusions: MRSA transmission dynamics between the ACH and
ILTCFs were complex. The greater diversity of STs in ILTCFs
suggests that the ecosystem in such settings might be more
conducive for intrafacility transmission events. ST22 and ST45
have successfully established themselves in ILTCFs. The
importance of interconnected infection prevention and control
measures and strategies cannot be overemphasized.",
journal = "Clin. Infect. Dis.",
volume = 64,
number = "suppl\_2",
pages = "S76--S81",
month = may,
year = 2017,
keywords = "MRSA; intermediate-care facilities; long-term care facilities.;
transmission; whole-genome
sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Canovas2016-ts,
title = "{Cross-Talk} between Staphylococcus aureus and Other
Staphylococcal Species via the agr Quorum Sensing System",
author = "Canovas, Jaime and Baldry, Mara and Bojer, Martin S and Andersen,
Paal S and Grzeskowiak, Piotr K and Stegger, Marc and Damborg,
Peter and Olsen, Christian A and Ingmer, Hanne",
abstract = "Staphylococci are associated with both humans and animals. While
most are non-pathogenic colonizers, Staphylococcus aureus is an
opportunistic pathogen capable of causing severe infections. S.
aureus virulence is controlled by the agr quorum sensing system
responding to secreted auto-inducing peptides (AIPs) sensed by
AgrC, a two component histidine kinase. agr loci are found also
in other staphylococcal species and for Staphylococcus
epidermidis, the encoded AIP represses expression of agr
regulated virulence genes in S. aureus. In this study we aimed to
better understand the interaction between staphylococci and S.
aureus, and show that this interaction may eventually lead to the
identification of new anti-virulence candidates to target S.
aureus infections. Here we show that culture supernatants of 37
out of 52 staphylococcal isolates representing 17 different
species inhibit S. aureus agr. The dog pathogen, Staphylococcus
schleiferi, expressed the most potent inhibitory activity and was
active against all four agr classes found in S. aureus. By
employing a S. aureus strain encoding a constitutively active AIP
receptor we show that the activity is mediated via agr.
Subsequent cloning and heterologous expression of the S.
schleiferi AIP in S. aureus demonstrated that this molecule was
likely responsible for the inhibitory activity, and further proof
was provided when pure synthetic S. schleiferi AIP was able to
completely abolish agr induction of an S. aureus reporter strain.
To assess impact on S. aureus virulence, we co-inoculated S.
aureus and S. schleiferi in vivo in the Galleria mellonella wax
moth larva, and found that expression of key S. aureus virulence
factors was abrogated. Our data show that the S. aureus agr locus
is highly responsive to other staphylococcal species suggesting
that agr is an inter-species communication system. Based on these
results we speculate that interactions between S. aureus and
other colonizing staphylococci will significantly influence the
ability of S. aureus to cause infection, and we propose that
other staphylococci are potential sources of compounds that can
be applied as anti-virulence therapy for combating S. aureus
infections.",
journal = "Front. Microbiol.",
volume = 7,
pages = "1733",
month = nov,
year = 2016,
keywords = "Staphylococcus aureus; Staphylococcus schleiferi; agr;
anti-virulence therapy; auto-inducing peptide; cross-talk; quorum
sensing; quorum sensing
inhibition;Staphylococcus;Papers\_for\_Michelle;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Roe2016-uc,
title = "Whole genome {SNP} typing to investigate methicillin-resistant
\textit{Staphylococcus aureus} carriage in a health-care provider
as the source of multiple surgical site infections",
author = "Roe, Chandler C and Horn, Kimberly S and Driebe, Elizabeth M and
Bowers, Jolene and Terriquez, Joel A and Keim, Paul and
Engelthaler, David M",
abstract = "BACKGROUND: Prevention of nosocomial transmission of infections
is a central responsibility in the healthcare environment, and
accurate identification of transmission events presents the first
challenge. Phylogenetic analysis based on whole genome sequencing
provides a high-resolution approach for accurately relating
isolates to one another, allowing precise identification or
exclusion of transmission events and sources for nearly all
cases. We sequenced 24 methicillin-resistant Staphylococcus
aureus (MRSA) genomes to retrospectively investigate a suspected
point source of three surgical site infections (SSIs) that
occurred over a one-year period. The source of transmission was
believed to be a surgical team member colonized with MRSA,
involved in all surgeries preceding the SSI cases, who was
subsequently decolonized. Genetic relatedness among isolates was
determined using whole genome single nucleotide polymorphism
(SNP) data. RESULTS: Whole genome SNP typing (WGST) revealed 283
informative SNPs between the surgical team member's isolate and
the closest SSI isolate. The second isolate was 286 and the third
was thousands of SNPs different, indicating the nasal carriage
strain from the surgical team member was not the source of the
SSIs. Given the mutation rates estimated for S. aureus, none of
the SSI isolates share a common ancestor within the past 16
years, further discounting any common point source for these
infections. The decolonization procedures and resources spent on
the point source infection control could have been prevented if
WGST was performed at the time of the suspected transmission,
instead of retrospectively. CONCLUSIONS: Whole genome sequence
analysis is an ideal method to exclude isolates involved in
transmission events and nosocomial outbreaks, and coupling this
method with epidemiological data can determine if a transmission
event occurred. These methods promise to direct infection control
resources more appropriately.",
journal = "Hereditas",
volume = 153,
pages = "11",
month = nov,
year = 2016,
keywords = "MRSA; Nasal carriage; Surgical site infections; Transmission;
Whole genome
sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Post2016-tm,
title = "Characterisation of nasal methicillin-resistant Staphylococcus
aureus isolated from international human and veterinary surgeons",
author = "Post, Virginia and Harris, Llinos and Morgenstern, Mario and
Richards, R Geoff and Sheppard, Samuel K and Moriarty, Fintan",
abstract = "Nasal colonization with methicillin-resistant Staphylococcus
aureus is poorly described for surgeons, despite the increased
exposure to nosocomial pathogens and at-risk patients. This study
investigated the molecular epidemiology and antimicrobial
resistance of 26 MRSA isolates cultured from the nares of an
international cross-sectional study of 1,166 human and 60
veterinary surgeons. All isolates were subjected to agr-, spa-
and MLST typing and the presence of 22 virulence factors were
screened for by PCR. Additionally, biofilm-forming ability,
haemolytic activity, staphyloxanthin production and antibiotic
resistance were determined. The genome of a rifampicin resistant
MRSA was sequenced. Approximately half of the isolates belonged
to well-described clonal lineages, ST1, ST5, ST8, ST45 and ST59,
that have been previously associated with severe infections and
increased patient mortality. Two of the 3 veterinarian MRSA
belonged to epidemic livestock-associated MRSA clonal lineages
(ST398 and ST8) previously associated with high transmission
potential between animals and humans. The isolates did not
display any consistent virulence gene pattern, and 35\% of the
isolates carried at least one of: the Panton-Valentine leukocidin
lukFS-PV; the exfoliative toxin eta; or the toxic shock syndrome
tst genes. Resistance to rifampicin was detected in one
veterinarian isolate, and was found to be due to 3 mutations in
the rpoB gene. Surgeons occupy a critical position in the
healthcare profession due to their close contact with patients.
In this study, surgeons were found to be colonized with MRSA at
low rates that are similar to the general population, and the
colonising strains were often common clonal lineages.",
journal = "J. Med. Microbiol.",
month = dec,
year = 2016,
keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Costa2013-dt,
title = "Complete genome sequence of a variant of the
methicillin-resistant Staphylococcus aureus {ST239} lineage,
strain {BMB9393}, displaying superior ability to accumulate
ica-independent biofilm",
author = "Costa, Maiana Oliveira Cerqueira and Beltrame, Cristiana
Ossaille and Ferreira, Fabienne Antunes and Botelho, Ana Maria
Nunes and Lima, Nicholas Costa Barroso and Souza, Rangel Celso
and de Almeida, Luiz Gonzaga Paula and Vasconcelos, Ana Tereza
Ribeiro and Nicol{\'a}s, Marisa Fabiana and Figueiredo, Agnes
Marie S{\'a}",
abstract = "ABSTRACT Biofilm is considered an important virulence factor in
nosocomial infections. Herein, we report the complete genome
sequence of a variant of methicillin-resistant Staphylococcus
aureus, strain BMB9393, which is highly disseminated in Brazil.
This ...",
journal = "Genome Announc.",
publisher = "Am Soc Microbiol",
volume = 1,
number = 4,
pages = "e00576--13",
year = 2013,
keywords = "Staphylococcus;experimental\_design;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Lee2017-xz,
title = "Emerging multidrug resistance in community-associated
Staphylococcus aureus involved in skin and soft tissue infections
and nasal colonization",
author = "Lee, Grace C and Dallas, Steven D and Wang, Yufeng and Olsen,
Randall J and Lawson, Kenneth A and Wilson, James and Frei,
Christopher R",
abstract = "Background:Staphylococcus aureus is a major pathogen causing
significant morbidity and mortality worldwide. The emergence of
MDR S. aureus strains in the community setting has major
implications in disease management. However, data regarding the
occurrence and patterns of MDR community-associated S. aureus
sub-clones is limited.Objectives: To use whole-genome sequences
to describe the diversity and distribution of resistance
mechanisms among community-associated S. aureus
isolates.Methods:S. aureus isolates from skin and soft tissue
infections (SSTIs) and nasal colonization were collected from
patients within 10 primary care clinics from 2007 to 2015. The
Illumina Miseq platform was used to determine the genome
sequences for 144 S. aureus isolates. Phylogenetic and
bioinformatics analyses were performed using in silico tools. The
resistome was assembled and compared with the phenotypically
derived antibiogram.Results: Approximately one-third of S. aureus
isolates in the South Texas primary care setting were MDR. A
higher proportion of SSTI isolates were MDR in comparison with
nasal colonization isolates. Individuals with MDR S. aureus SSTIs
were more likely to be African American and obese. Furthermore,
S. aureus populations are able to acquire and lose antimicrobial
resistance genes. USA300 strains were differentiated by a stable
chromosomal mutation in gyrA conferring quinolone resistance. The
resistomes were highly predictive of antimicrobial resistance
phenotypes.Conclusions: These findings highlight the high
prevalence and epidemiological factors associated with MDR S.
aureus strains in the community setting and demonstrate the
utility of next-generation sequencing to potentially quicken
antimicrobial resistance detection and surveillance for targeted
interventions.",
journal = "J. Antimicrob. Chemother.",
month = jul,
year = 2017,
keywords = "staphylococcus aureus; drug resistance, microbial; nose; skin and
soft tissue infections; microbial colonization; community; drug
resistance, multiple; phenotype; genome; genes; mutation; clone
cells; african american; chromosomes; obesity; primary health
care; disease management; surveillance, medical;
antibiogram;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Bayer2016-hc,
title = "Dysregulation of mprF and {dltABCD} expression among
daptomycin-non-susceptible {MRSA} clinical isolates",
author = "Bayer, Arnold S and Mishra, Nagendra N and Cheung, Ambrose L and
Rubio, Aileen and Yang, Soo-Jin",
abstract = "BACKGROUND: In small series or individual reports, SNPs within
the mprF ORF and dysregulation of its expression in
Staphylococcus aureus have been linked to daptomycin resistance
(DAP-R) via a proposed gain-in-function mechanism. Similarly,
dysregulation of dltABCD has also been associated with DAP-R.
METHODS: Using 22 well-characterized, isogenic
daptomycin-susceptible (DAP-S)/DAP-R clinical MRSA strain pairs,
we assessed potential relationships of the DAP-R phenotype with:
(i) regulation of mprF transcription; (ii) regulation of dltABCD
transcription; (iii) expression of the two-component regulatory
system, graRS (upstream regulator for both mprF and dltABCD
transcription); (iv) SNPs within the graRS promoter or its ORF;
and (v) altered mprF transcription and lysyl-phosphatidylglycerol
(L-PG) synthesis. RESULTS: Enhanced expression of mprF occurred
with SNPs in highly distinct and well-chronicled MprF domain 'hot
spots' and rarely occurred without such mutations. Increased
expression and/or dysregulation of mprF and dltABCD were not
uncommon in DAP-R strains, occurring in 27\% of strains for each
gene. In these latter strains, neither graRS expression profiles
nor polymorphic sequences within the graRS promoter or ORF could
be significantly linked to altered transcription of mprF or dlt.
CONCLUSIONS: Although graRS can co-regulate mprF and dltABCD
expression, loci outside of this regulon appear to be involved in
dysregulation of these latter two genes and the DAP-R phenotype.
Finally, DAP-R strains exhibiting significantly altered mprF
transcription profiles produced significantly increased levels of
L-PG.",
journal = "J. Antimicrob. Chemother.",
volume = 71,
number = 8,
pages = "2100--2104",
month = aug,
year = 2016,
keywords = "confirmed\_SA-resistance-mutation;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Stevens2017-ff,
title = "Draft Genome Sequence of \textit{Staphylococcus aureus} S681, a
{Tetracycline-Sensitive} {Livestock-Associated}
{Methicillin-Resistant} Clonal Complex 398 Strain",
author = "Stevens, Marc J A and Stephan, Roger and Johler, Sophia",
abstract = "We present the draft genome sequence of an atypical
tetracycline-susceptible livestock-associated
methicillin-resistant Staphylococcus aureus (MRSA) strain. It
contains 2,817,340 bp and 2,858 coding sequences, including 6
rRNA operons, 56 tRNAs, and 4 noncoding RNA (ncRNA) genes. The
strain harbors a tet(M) gene, but 15 point mutations in amino
acids are present that likely impair the functionality of TetM.",
journal = "Genome Announc.",
volume = 5,
number = 33,
month = aug,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Ugolotti2017-fa,
title = "Genomic characterization of a paediatric {MRSA} outbreak by Next
Generation Sequencing",
author = "Ugolotti, Elisabetta and Di Marco, Eddi and Bandettini, Roberto
and Biassoni, Roberto",
abstract = "INTRODUCTION: Twelve strains of meticillin-resistant
Staphylococcus aureus (MRSA) isolated during a suspected outbreak
in a Paediatric Intensive Care Unit were analyzed by Whole Genome
Sequence (WGS). AIM: To define the clonality of MRSA strains to a
high discriminative power and to evaluate the presence of genetic
determinants responsible for antibiotic resistance and for
virulence. RESULTS: Ten out of 12 strains belonged to the MLST
ST2625, while the other two were ST8. Among the ST2625 strains,
analysis based on 1126 genes showed that they were clonal sharing
more than 98.3\% of allelic identities and one of them was
isolated from a health care worker. All the ST2625 strains were
characterized by a SCC-Mec cassette IVa and the Resistoma
analysis indicated a correspondence between phenotypic and
genotypic characteristics. The study of 63 genes associated with
the virulence was correlated to the pattern of clonality shown.
CONCLUSION: This analysis confirmed the occurrence of an
outbreak, which allowed us to strictly enforce standard infection
control measures that promptly terminated the outbreak.",
journal = "J. Hosp. Infect.",
month = aug,
year = 2017,
keywords = "MRSA; Paediatric Nosocomial Infections; Resistoma; Staphylococcus
aureus; Toxoma; Whole-genome
sequencing;Staphylococcus;transmission-epidemiology;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Satoo2017-ue,
title = "Complete Sequence of a \textit{Staphylococcus aureus} Clonal
Complex 81 Strain, the Dominant Lineage in Food Poisoning
Outbreaks in Japan",
author = "Sato'o, Yusuke and Hisatsune, Junzo and Hirakawa, Hideki and Ono,
Hisaya K and Omoe, Katsuhiko and Sugai, Motoyuki",
abstract = "Staphylococcus aureus No. 10 is an isolate from a staphylococcal
food poisoning outbreak in Japan, classified as clonal complex 81
subtype 1. It preferentially produces larger quantities of
staphylococcal enterotoxin A (SEA) and staphylococcal enterotoxin
H (SEH) in foods and media. Here, we report the complete
annotated genome sequence of the chromosome and a plasmid.",
journal = "Genome Announc.",
volume = 5,
number = 34,
month = aug,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Sivaraman2017-uf,
title = "Draft Genome Sequence of a {Methicillin-Resistant}
\textit{Staphylococcus aureus} Isolate (Sequence Type 1) from
Seafood",
author = "Sivaraman, G K and Vanik, Deesha and Visnuvinayagam, S and
Prasad, M M and Ravishankar, C N",
abstract = "The draft genome sequence of a methicillin-resistant
Staphylococcus aureus (MRSA) isolate (sequence type 1 [ST 1])
from the salted dried ribbonfish from Gujarat, India, is reported
here. Staphylococcus genus-specific genes were present in this
MRSA isolate. The whole-genome sequence of this strain contains
2,797 protein-coding genes and 80 RNAs within the 2.85-Mb genome.",
journal = "Genome Announc.",
volume = 5,
number = 34,
month = aug,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Lee2017-lr,
title = "Emerging multidrug resistance in community-associated
Staphylococcus aureus involved in skin and soft tissue infections
and nasal colonization",
author = "Lee, Grace C and Dallas, Steven D and Wang, Yufeng and Olsen,
Randall J and Lawson, Kenneth A and Wilson, James and Frei,
Christopher R",
abstract = "Background: Staphylococcus aureus is a major pathogen causing
significant morbidity and mortality worldwide. The emergence of
MDR S. aureus strains in the community setting has major
implications in disease management. However, data regarding the
occurrence and patterns of MDR community-associated S. aureus
sub-clones is limited. Objectives: To use whole-genome sequences
to describe the diversity and distribution of resistance
mechanisms among community-associated S. aureus isolates.
Methods: S. aureus isolates from skin and soft tissue infections
(SSTIs) and nasal colonization were collected from patients
within 10 primary care clinics from 2007 to 2015. The Illumina
Miseq platform was used to determine the genome sequences for 144
S. aureus isolates. Phylogenetic and bioinformatics analyses were
performed using in silico tools. The resistome was assembled and
compared with the phenotypically derived antibiogram. Results:
Approximately one-third of S. aureus isolates in the South Texas
primary care setting were MDR. A higher proportion of SSTI
isolates were MDR in comparison with nasal colonization isolates.
Individuals with MDR S. aureus SSTIs were more likely to be
African American and obese. Furthermore, S. aureus populations
are able to acquire and lose antimicrobial resistance genes.
USA300 strains were differentiated by a stable chromosomal
mutation in gyrA conferring quinolone resistance. The resistomes
were highly predictive of antimicrobial resistance phenotypes.
Conclusions: These findings highlight the high prevalence and
epidemiological factors associated with MDR S. aureus strains in
the community setting and demonstrate the utility of
next-generation sequencing to potentially quicken antimicrobial
resistance detection and surveillance for targeted interventions.",
journal = "J. Antimicrob. Chemother.",
volume = 72,
number = 9,
pages = "2461--2468",
month = sep,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Hansen2017-hf,
title = "Whole Genome Sequencing of Danish \textit{Staphylococcus
argenteus} Reveals a Genetically Diverse Collection with Clear
Separation from \textit{Staphylococcus aureus}",
author = "Hansen, Thomas A and Bartels, Mette D and H{\o}gh, Silje V and
Dons, Lone E and Pedersen, Michael and Jensen, Th{\o}ger G and
Kemp, Michael and Skov, Marianne N and Gumpert, Heidi and
Worning, Peder and Westh, Henrik",
abstract = "Staphylococcus argenteus (S. argenteus) is a newly identified
Staphylococcus species that has been misidentified as
Staphylococcus aureus (S. aureus) and is clinically relevant. We
identified 25 S. argenteus genomes in our collection of whole
genome sequenced S. aureus. These genomes were compared to
publicly available genomes and a phylogeny revealed seven
clusters corresponding to seven clonal complexes. The genome of
S. argenteus was found to be different from the genome of S.
aureus and a core genome analysis showed that ~33\% of the total
gene pool was shared between the two species, at 90\% homology
level. An assessment of mobile elements shows flow of SCCmec
cassettes, plasmids, phages, and pathogenicity islands, between
S. argenteus and S. aureus. This dataset emphasizes that S.
argenteus and S. aureus are two separate species that share
genetic material.",
journal = "Front. Microbiol.",
volume = 8,
pages = "1512",
month = aug,
year = 2017,
keywords = "S. argenteus; S. aureus; SargPI; SargPID7903; Staphylococcus;
phage;
plasmid;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Jo2016-qi,
title = "Phenotypic and genotypic characterisation of multiple
antibiotic-resistant Staphylococcus aureus exposed to
subinhibitory levels of oxacillin and levofloxacin",
author = "Jo, Ara and Ahn, Juhee",
abstract = "BACKGROUND: The emergence and spread of multidrug resistant
methicillin-resistant Staphylococcus aureus (MDR-MRSA) has
serious health consequences in the presence of sub-MIC
antibiotics. Therefore, this study was designed to evaluate
$\beta$-lactamase activity, efflux activity, biofilm formation,
and gene expression pattern in Staphylococcus aureus KACC 10778,
S. aureus ATCC 15564, and S. aureus CCARM 3080 exposed to
sublethal concentrations of levofloxacin and oxacillin. RESULTS:
The decreased MICs were observed in S. aureus KACC and S. aureus
ATCC when exposed to levofloxacin and oxacillin, while and S.
aureus CCARM remained resistance to streptomycin (512 $\mu$g/mL)
in the presence of levofloxacin and imipenem (>512 $\mu$g/mL) in
the presence of oxacillin. The considerable increase in
extracellular and membrane-bound $\beta$-lactamase activities was
observed in S. aureus ATCC exposed to oxacillin (>26
$\mu$mol/min/mL). The antibiotic susceptibility of all strains
exposed to EPIs (CCCP and PA$\beta$N) varied depending on the
classes of antibiotics. The relative expression levels of
adhesion-related genes (clfA, clfB, fnbA, fnnB, and icaD),
efflux-related genes (norB, norC, and qacA/B), and enterotoxin
gene (sec) were increased more than 5-fold in S. aureus CCARM.
The eno and qacA/B genes were highly overexpressed by more than
12- and 9-folds, respectively, in S. aureus CCARM exposed to
levofloxacin. The antibiotic susceptibility, lactamase activity,
biofilm-forming ability, efflux activity, and gene expression
pattern varied with the intrinsic antibiotic resistance of S.
aureus KACC, S. aureus ATCC, and S. aureus CCARM exposed to
levofloxacin and oxacillin. CONCLUSIONS: This study would provide
useful information for better understating of combination therapy
related to antibiotic resistance mechanisms and open the door for
designing effective antibiotic treatment protocols to prevent
excessive use of antibiotics in clinical practice.",
journal = "BMC Microbiol.",
volume = 16,
number = 1,
pages = "170",
month = jul,
year = 2016,
keywords = "Antibiotic resistance; Biofilm; Efflux pump; Gene expression;
Lactamase; Levofloxacin; Oxacillin; Staphylococcus
aureus;Staphylococcus;antibiotics;oxacillin;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Hisatsune2017-ce,
title = "Complete Genome Sequence of Systemically Disseminated Sequence
Type 8 Staphylococcal Cassette Chromosome \textit{mec} Type {IVl}
{Community-Acquired} {Methicillin-Resistant}
\textit{Staphylococcus aureus}",
author = "Hisatsune, Junzo and Hagiya, Hideharu and Shiota, Sumiko and
Sugai, Motoyuki",
abstract = "Staphylococcus aureus JH4899, a community-acquired
methicillin-resistant Staphylococcus aureus (CA-MRSA) isolate
collected from a patient with systematically disseminated
infection, is classified as sequence type 8 and carries the
staphylococcal cassette chromosome mec type IVl (SCCmecIVl). It
produces TSST-1, SEC, a newly discovered enterotoxin (SE1), and
epidermal cell differentiation inhibitor A (EDIN-A). Here, we
present the complete genome sequence of the chromosome and a
plasmid harboring the se1 and ednA genes.",
journal = "Genome Announc.",
volume = 5,
number = 35,
month = aug,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Zhang2017-bb,
title = "Genome Sequence of \textit{Staphylococcus aureus} {PX03}, an
{Acetoin-Producing} Strain with a {Small-Sized} Genome",
author = "Zhang, Ge and Wang, Qian and Su, Yulong and Li, Shugui and Liu,
Haobao",
abstract = "Staphylococcus aureus PX03 can produce acetoin efficiently. Here,
we present a 2.38-Mb assembly of its genome sequence, which might
provide further insights into the molecular mechanism of its
acetoin biosynthesis to further improve its biotechnological
applications.",
journal = "Genome Announc.",
volume = 5,
number = 37,
month = sep,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Lebughe2017-qk,
title = "The Impact of the \textit{Staphylococcus aureus} Virulome on
Infection in a Developing Country: A Cohort Study",
author = "Lebughe, Marthe and Phaku, Patrick and Niemann, Silke and Mumba,
Dieudonn{\'e} and Peters, Georg and Muyembe-Tamfum, Jean-Jacques
and Mellmann, Alexander and Strau{\ss}, Lena and Schaumburg,
Frieder",
abstract = "We performed a cohort study to analyze the virulome of
Staphylococcus aureus from the Democratic Republic of the Congo
using whole genome sequencing and to assess its impact on the
course of S. aureus infections. Community-associated S. aureus
from nasal colonization (n = 100) and infection (n = 86) were
prospectively collected. Phenotypic susceptibility testing and
WGS was done for each isolate. WGS data were used to screen for
79 different virulence factors and for genotyping purposes (spa
typing, multilocus sequence typing). The majority of the 79
virulence factors were equally distributed among isolates from
colonization and infection. Panton-Valentine leukocidin (PVL) and
the non-truncated hemolysin $\beta$ were associated with skin and
soft tissue infection (SSTI) and recurrence of disease but did
not influence the course of infection (i.e., mortality, surgical
intervention). For the first time, we show that not only PVL but
also hemolysin $\beta$ could contribute to the development of
SSTI in PVL-endemic areas such as Africa.",
journal = "Front. Microbiol.",
volume = 8,
pages = "1662",
month = aug,
year = 2017,
keywords = "Africa; Staphylococcus aureus; infection; virulome; whole genome
sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Sassi2017-mx,
title = "An outbreak in intravenous drug users due to {USA300}
{Latin-American} variant community-acquired methicillin-resistant
Staphylococcus aureus in France as early as 2007",
author = "Sassi, M and Felden, B and Revest, M and Tattevin, P and
Augagneur, Y and Donnio, P-Y",
abstract = "Intravenous drug users are at increased risk of Staphylococcus
aureus infections. Most cases are related to clones prevalent in
the community. We report an outbreak of community-acquired
methicillin-resistant Staphylococcus aureus infections that
occurred from 2007 to 2009 in intravenous drug users and their
close contacts in Northwestern France. Clinical and molecular
investigations suggested that the clones were more similar than
those usually isolated in the American continent although none of
the patients traveled abroad or had contact with individuals who
had traveled to the Americas. Then, a retrospective whole genome
sequencing and phylogenetic analyses demonstrated that the
strains isolated from the first case belong to the USA300
Latin-American variant clone, based on the absence of arginine
catabolic mobile element (ACME), and the presence of copper and
mercury resistance mobile element (COMER), a distinctive feature
of the South American variant. Our study shows genetic evidence
for introduction of this clone as early as 2007 in France. This
report also illustrates the importance of genome sequencing to
finely characterize and monitor the emergence of unexpected S.
aureus clones among high-risk populations, especially when living
in promiscuity.",
journal = "Eur. J. Clin. Microbiol. Infect. Dis.",
month = sep,
year = 2017,
keywords = "Staphylococcus;transmission-epidemiology;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Katayama2017-uq,
title = "Prevalence of Slow-growth Vancomycin Non-susceptibility In
Methicillin-resistant Staphylococcus aureus",
author = "Katayama, Yuki and Azechi, Takuya and Miyazaki, Motoyasu and
Takata, Tohru and Sekine, Miwa and Matsui, Hidehito and Hanaki,
Hideaki and Yahara, Koji and Sasano, Hiroshi and Asakura, Kota
and Takaku, Tomoiku and Ochiai, Tomonori and Komatsu, Norio and
Chambers, Henry F",
abstract = "We have previsously reported a novel phenotype of
vancomycin-intermediate Staphylococcus aureus (VISA) strains,
``slow-VISA,'' in which colonies appear only after 72 h of
incubation. Slow-VISA strains can be difficult to detect because
prolonged incubation is required and the phenotype is unstable.
To develop a method for detection of slow-VISA isolates, we
studied 23 slow-VISA isolates derived from heteroVISA clinical
strain Mu3. We identified single nucleotide polymorphisms (SNP)
in genes involved in various pathways such as purine/pyrimidine
synthesis, cell metabolism, and cell-wall peptidoglycan
synthesis, which have been implicated in the stringent response.
We found that mupirocin, which also induces a stringent response,
caused stable expression of vancomycin resistance. On the basis
of these results, we developed a method for detection of
slow-VISA using mupirocin 0.032 $\mu$g/ml (Patent Application No.
PCT/JP2017/008975filed on March 7, 2017). Using this method, we
detected 53 (15.6\%) slow-VISA isolates among clinical
methicillin-resistant S.aureus (MRSA) isolates. In contrast, the
VISA phenotype was detected in fewer than 1\% of isolates.
Deep-sequencing analysis showed that slow-VISA clones are present
in small numbers among hVISA isolates, and proliferate in the
presence of vancomycin. This slow-VISA subpopulation could
account in part for the recurrence and persistence of MRSA
infection.",
journal = "Antimicrob. Agents Chemother.",
month = aug,
year = 2017,
keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Stanczak-Mrozek2015-ds,
title = "Within-host diversity of {MRSA} antimicrobial resistances",
author = "Stanczak-Mrozek, Kinga I and Manne, Anusha and Knight, Gwenan M
and Gould, Katherine and Witney, Adam A and Lindsay, Jodi A",
abstract = "OBJECTIVES: MRSA is a major antimicrobial resistance (AMR)
pathogen. The reservoir of infecting isolates is colonization,
which is the site of evolutionary selection. The aim was to
identify if AMRs in colonizing MRSA populations diversified and
potential mechanisms of resistance gene transfer in vivo.
METHODS: Nasal swabs from 38 MRSA carriers admitted to hospital
were plated and 20 individual colonies from each patient tested
for phenotypic antibiotic susceptibility and genetically for
lineage, carriage of four prophages and three plasmid families.
Free bacteriophages were detected in swabs as well as their
capacity for transducing resistance genes. RESULTS: Nine (24\%)
patients carried phenotypic AMR variants and 24 (63\%) carried
prophage and plasmid variants. If a single colony was selected
for testing, the probability of detecting all AMR in that patient
was 87\%. Sixty-four different AMR and mobile genetic element
(MGE) profiles were detected, mostly in the MRSA CC22 background
(where CC stands for clonal complex), with up to 8 profiles per
patient. Nearly half of the patients carried detectable free
bacteriophages and phages successfully transduced resistance
genes between laboratory and patient isolates in vitro. WGS
showed MRSA core genomes were stable, while AMR and MGEs varied.
CONCLUSIONS: 'Clouds' of MRSA variants that have acquired or lost
AMR and MGEs are common in nasal colonizing populations and
bacteriophages may play an important role in gene transfer.
Accurate estimation of AMR and genetic variability has
implications for diagnostics, epidemiology, antimicrobial
stewardship and understanding the evolutionary selection of AMR
in colonizing populations.",
journal = "J. Antimicrob. Chemother.",
volume = 70,
number = 8,
pages = "2191--2198",
month = aug,
year = 2015,
keywords = "horizontal gene transfer; mobile genetic elements; transduction;
whole-genome
sequencing;Staphylococcus;bacerial\_genetics;colonization;phage;Staph\_evolutionary\_history;Staph\_evolutionary\_history/staph
microbial
interactions;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Aanensen2016-lz,
title = "{Whole-Genome} Sequencing for Routine Pathogen Surveillance in
Public Health: a Population Snapshot of Invasive Staphylococcus
aureus in Europe",
author = "Aanensen, David M and Feil, Edward J and Holden, Matthew T G and
Dordel, Janina and Yeats, Corin A and Fedosejev, Artemij and
Goater, Richard and Castillo-Ram{\'\i}rez, Santiago and Corander,
Jukka and Colijn, Caroline and Chlebowicz, Monika A and Schouls,
Leo and Heck, Max and Pluister, Gerlinde and Ruimy, Raymond and
Kahlmeter, Gunnar and {\AA}hman, Jenny and Matuschek, Erika and
Friedrich, Alexander W and Parkhill, Julian and Bentley, Stephen
D and Spratt, Brian G and Grundmann, Hajo and {European SRL
Working Group}",
abstract = "UNLABELLED: The implementation of routine whole-genome sequencing
(WGS) promises to transform our ability to monitor the emergence
and spread of bacterial pathogens. Here we combined WGS data from
308 invasive Staphylococcus aureus isolates corresponding to a
pan-European population snapshot, with epidemiological and
resistance data. Geospatial visualization of the data is made
possible by a generic software tool designed for public health
purposes that is available at the project URL
(http://www.microreact.org/project/EkUvg9uY?tt=rc). Our analysis
demonstrates that high-risk clones can be identified on the basis
of population level properties such as clonal relatedness,
abundance, and spatial structuring and by inferring virulence and
resistance properties on the basis of gene content. We also show
that in silico predictions of antibiotic resistance profiles are
at least as reliable as phenotypic testing. We argue that this
work provides a comprehensive road map illustrating the three
vital components for future molecular epidemiological
surveillance: (i) large-scale structured surveys, (ii) WGS, and
(iii) community-oriented database infrastructure and analysis
tools. IMPORTANCE: The spread of antibiotic-resistant bacteria is
a public health emergency of global concern, threatening medical
intervention at every level of health care delivery. Several
recent studies have demonstrated the promise of routine
whole-genome sequencing (WGS) of bacterial pathogens for
epidemiological surveillance, outbreak detection, and infection
control. However, as this technology becomes more widely adopted,
the key challenges of generating representative national and
international data sets and the development of bioinformatic
tools to manage and interpret the data become increasingly
pertinent. This study provides a road map for the integration of
WGS data into routine pathogen surveillance. We emphasize the
importance of large-scale routine surveys to provide the
population context for more targeted or localized investigation
and the development of open-access bioinformatic tools to provide
the means to combine and compare independently generated data
with publicly available data sets.",
journal = "MBio",
volume = 7,
number = 3,
month = may,
year = 2016,
keywords = "cloning;Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Reuter2016-yp,
title = "Building a genomic framework for prospective {MRSA} surveillance
in the United Kingdom and the Republic of Ireland",
author = "Reuter, Sandra and T{\"o}r{\"o}k, M Est{\'e}e and Holden, Matthew
T G and Reynolds, Rosy and Raven, Kathy E and Blane, Beth and
Donker, Tjibbe and Bentley, Stephen D and Aanensen, David M and
Grundmann, Hajo and Feil, Edward J and Spratt, Brian G and
Parkhill, Julian and Peacock, Sharon J",
abstract = "The correct interpretation of microbial sequencing data applied
to surveillance and outbreak investigation depends on accessible
genomic databases to provide vital genetic context. Our aim was
to construct and describe a United Kingdom MRSA database
containing over 1000 methicillin-resistant Staphylococcus aureus
(MRSA) genomes drawn from England, Northern Ireland, Wales,
Scotland, and the Republic of Ireland over a decade. We sequenced
1013 MRSA submitted to the British Society for Antimicrobial
Chemotherapy by 46 laboratories between 2001 and 2010. Each
isolate was assigned to a regional healthcare referral network in
England and was otherwise grouped based on country of origin.
Phylogenetic reconstructions were used to contextualize MRSA
outbreak investigations and to detect the spread of resistance.
The majority of isolates (n = 783, 77\%) belonged to CC22, which
contains the dominant United Kingdom epidemic clone (EMRSA-15).
There was marked geographic structuring of EMRSA-15, consistent
with widespread dissemination prior to the sampling decade
followed by local diversification. The addition of MRSA genomes
from two outbreaks and one pseudo-outbreak demonstrated the
certainty with which outbreaks could be confirmed or refuted. We
identified local and regional differences in antibiotic
resistance profiles, with examples of local expansion, as well as
widespread circulation of mobile genetic elements across the
bacterial population. We have generated a resource for the future
surveillance and outbreak investigation of MRSA in the United
Kingdom and Ireland and have shown the value of this during
outbreak investigation and tracking of antimicrobial resistance.",
journal = "Genome Res.",
volume = 26,
number = 2,
pages = "263--270",
month = feb,
year = 2016,
keywords = "Staphylococcus;Staph\_evolutionary\_history/staph microbial
interactions;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Staph\_evolution\_toxins",
language = "en"
}
@ARTICLE{Dekker2016-rk,
title = "{Next-Generation} Epidemiology: Using {Real-Time} Core Genome
Multilocus Sequence Typing To Support Infection Control Policy",
author = "Dekker, John P and Frank, Karen M",
abstract = "Multidrug-resistant bacteria are responsible for substantial
morbidity and mortality worldwide. Tracking the nosocomial spread
of resistant bacteria is critical to infection control. Mellmann
et al. (J. Clin. Microbiol. 54:2874-2881, 2016,
http://dx.doi.org/10.1128/JCM.00790-16) have described
prospective whole-genome sequencing with core genome multilocus
sequencing typing (cgMLST) analysis for real-time surveillance
and have addressed the practical aspects of implementing this
type of operation in the hospital setting.",
journal = "J. Clin. Microbiol.",
volume = 54,
number = 12,
pages = "2850--2853",
month = dec,
year = 2016,
keywords = "Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers;Anti-infectives\_course",
language = "en"
}
@ARTICLE{Hau2017-rx,
title = "Draft Genome Sequences of Nine {Livestock-Associated}
{Methicillin-Resistant} \textit{Staphylococcus aureus} Sequence
Type 5 Isolates Obtained from Humans after {Short-Term} Swine
Contact",
author = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and Frana,
Timothy S and Nicholson, Tracy L",
abstract = "Livestock-associated methicillin-resistant Staphylococcus aureus
(LA-MRSA) sequence type 5 (ST5) has raised concerns surrounding
the potential for these isolates to colonize or cause disease in
humans with swine contact. Here, we report draft genome sequences
for nine LA-MRSA ST5 isolates obtained from humans after short
term swine contact.",
journal = "Genome Announc.",
volume = 5,
number = 41,
month = oct,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Donker2017-qu,
title = "Population genetic structuring of methicillin-resistant
\textit{Staphylococcus aureus} clone {EMRSA-15} within {UK}
reflects patient referral patterns",
author = "Donker, Tjibbe and Reuter, Sandra and Scriberras, James and
Reynolds, Rosy and Brown, Nicholas M and T{\"o}r{\"o}k, M
Est{\'e}e and James, Richard and Network, East Of England
Microbiology Research and Aanensen, David M and Bentley, Stephen
D and Holden, Matthew T G and Parkhill, Julian and Spratt, Brian
G and Peacock, Sharon J and Feil, Edward J and Grundmann, Hajo",
abstract = "Antibiotic resistance forms a serious threat to the health of
hospitalised patients, rendering otherwise treatable bacterial
infections potentially life-threatening. A thorough understanding
of the mechanisms by which resistance spreads between patients in
different hospitals is required in order to design effective
control strategies. We measured the differences between bacterial
populations of 52 hospitals in the United Kingdom and Ireland,
using whole-genome sequences from 1085 MRSA clonal complex 22
isolates collected between 1998 and 2012. The genetic differences
between bacterial populations were compared with the number of
patients transferred between hospitals and their regional
structure. The MRSA populations within single hospitals, regions
and countries were genetically distinct from the rest of the
bacterial population at each of these levels. Hospitals from the
same patient referral regions showed more similar MRSA
populations, as did hospitals sharing many patients. Furthermore,
the bacterial populations from different time-periods within the
same hospital were generally more similar to each other than
contemporaneous bacterial populations from different hospitals.
We conclude that, while a large part of the dispersal and
expansion of MRSA takes place among patients seeking care in
single hospitals, inter-hospital spread of resistant bacteria is
by no means a rare occurrence. Hospitals are exposed to constant
introductions of MRSA on a number of levels: (1) most MRSA is
received from hospitals that directly transfer large numbers of
patients, while (2) fewer introductions happen between regions or
(3) across national borders, reflecting lower numbers of
transferred patients. A joint coordinated control effort between
hospitals, is therefore paramount for the national control of
MRSA, antibiotic-resistant bacteria and other hospital-associated
pathogens.",
journal = "Microb Genom",
volume = 3,
number = 7,
pages = "e000113",
month = jul,
year = 2017,
keywords = "MRSA; antimicrobial Resistance; hospital
network;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Yu2017-kx,
title = "Complete Genome Sequence of Super {Biofilm-Elaborating}
\textit{Staphylococcus aureus} Isolated in Japan",
author = "Yu, Liansheng and Hisatsune, Junzo and Hirakawa, Hideki and
Mizumachi, Emiri and Toyoda, Atsushi and Yahara, Koji and Sugai,
Motoyuki",
abstract = "Staphylococcus aureus JP080, previously named TF2758, is a
clinical isolate from an atheroma and a super biofilm-elaborating
strain whose biofilm elaboration is dependent solely on
polysaccharide poly-N-acetylglucosamine/polysaccharide
intercellular adhesin (PNAG/PIA). Here, we report the complete
genome sequence of strain JP080, which consists of one chromosome
and one circular plasmid.",
journal = "Genome Announc.",
volume = 5,
number = 41,
month = oct,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Hau2017-mo,
title = "Draft Genome Sequences of Nine {Livestock-Associated}
{Methicillin-Resistant} \textit{Staphylococcus aureus} Sequence
Type 5 Isolates from Humans with {Long-Term} Swine Contact",
author = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and
Davies, Peter R and Haan, Jisun S and Nicholson, Tracy L",
abstract = "Humans have been found to harbor livestock-associated
methicillin-resistant Staphylococcus aureus (LA-MRSA) isolates.
LA-MRSA isolates are considered adapted to colonizing livestock
and less pathogenic in humans than their hospital- and
community-acquired counterparts. Here, we present nine LA-MRSA
sequence type 5 isolates from veterinarians with long-term swine
contact.",
journal = "Genome Announc.",
volume = 5,
number = 41,
month = oct,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Toleman2017-de,
title = "Investigation of a Cluster of Sequence Type 22
{Methicillin-Resistant} Staphylococcus aureus Transmission in a
Community Setting",
author = "Toleman, Michelle S and Watkins, Emmeline R and Williams, Tom and
Blane, Beth and Sadler, Belinda and Harrison, Ewan M and Coll,
Francesc and Parkhill, Julian and Nazareth, Bernadette and Brown,
Nicholas M and Peacock, Sharon J",
abstract = "BackgroundWhole-genome sequencing (WGS) has typically been used
to confirm or refute hospital/ward outbreaks of
methicillin-resistant Staphylococcus aureus (MRSA) identified
through routine practice. However, appropriately targeted WGS
strategies that identify routinely ``undetectable'' transmission
remain the ultimate aim.MethodsWGS of MRSA isolates sent to a
regional microbiological laboratory was performed as part of a
12-month prospective observational study. Phylogenetic analyses
identified a genetically related cluster of E-MRSA15 isolated
from patients registered to the same general practice (GP)
surgery. This led to an investigation to identify epidemiological
links, find additional cases, and determine potential for ongoing
transmission.ResultsWe identified 15 MRSA-positive individuals
with 27 highly related MRSA isolates who were linked to the GP
surgery, 2 of whom died with MRSA bacteremia. Of the 13 cases
that were further investigated, 11 had attended a leg
ulcer/podiatry clinic. Cases lacked epidemiological links to
hospitals, suggesting that transmission occurred elsewhere.
Environmental and staff screening at the GP surgery did not
identify an ongoing source of infection.ConclusionsSurveillance
in the United Kingdom shows that the proportion of MRSA
bacteremias apportioned to hospitals is decreasing, suggesting
the need for greater focus on the detection of MRSA outbreaks and
transmission in the community. This case study confirms that the
typically nosocomial lineage (E-MRSA15) can transmit within
community settings. Our study exemplifies the continued
importance of WGS in detecting outbreaks, including those which
may be missed by routine practice, and suggests that universal
WGS of bacteremia isolates may help detect outbreaks in
low-surveillance settings.",
journal = "Clin. Infect. Dis.",
month = oct,
year = 2017,
keywords = "genome; methicillin-resistant staphylococcus aureus; community;
disease outbreaks; surgical procedures, operative;
bacteremia;Staphylococcus;grants;interesting;transmission-epidemiology;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Coll_undated-fs,
title = "and the community",
author = "Coll, Francesc and Harrison, Ewan M and Toleman, Michelle S and
Reuter, Sandra and Raven, Kathy E and Blane, Beth and Palmer,
Beverley and Kappeler, A Ruth M and Brown, Nicholas M and
Est{\'e}e T{\"o}r{\"o}k, M and Parkhill, Julian and Peacock,
Sharon J",
keywords = "transmission-epidemiology;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Donker2017-qu,
title = "Population genetic structuring of methicillin-resistant
\textit{Staphylococcus aureus} clone {EMRSA-15} within {UK}
reflects patient referral patterns",
author = "Donker, Tjibbe and Reuter, Sandra and Scriberras, James and
Reynolds, Rosy and Brown, Nicholas M and Est{\'e}e
T{\"o}r{\"o}k, M and James, Richard and {East of England
Microbiology Research Network} and Aanensen, David M and
Bentley, Stephen D and Holden, Matthew T G and Parkhill, Julian
and Spratt, Brian G and Peacock, Sharon J and Feil, Edward J and
Grundmann, Hajo",
abstract = "Antibiotic resistance forms a serious threat to the health of
hospitalised patients, rendering otherwise treatable bacterial
infections potentially life-threatening. A thorough
understanding of the mechanisms by which resistance spreads
between patients in different hospitals is required in order to
design effective control strategies. We measured the differences
between bacterial populations of 52 hospitals in the United
Kingdom and Ireland, using whole-genome sequences from 1085 MRSA
clonal complex 22 isolates collected between 1998 and 2012. The
genetic differences between bacterial populations were compared
with the number of patients transferred between hospitals and
their regional structure. The MRSA populations within single
hospitals, regions and countries were genetically distinct from
the rest of the bacterial population at each of these levels.
Hospitals from the same patient referral regions showed more
similar MRSA populations, as did hospitals sharing many
patients. Furthermore, the bacterial populations from different
time-periods within the same hospital were generally more
similar to each other than contemporaneous bacterial populations
from different hospitals. We conclude that, while a large part
of the dispersal and expansion of MRSA takes place among
patients seeking care in single hospitals, inter-hospital spread
of resistant bacteria is by no means a rare occurrence.
Hospitals are exposed to constant introductions of MRSA on a
number of levels: (1) most MRSA is received from hospitals that
directly transfer large numbers of patients, while (2) fewer
introductions happen between regions or (3) across national
borders, reflecting lower numbers of transferred patients. A
joint coordinated control effort between hospitals, is therefore
paramount for the national control of MRSA, antibiotic-resistant
bacteria and other hospital-associated pathogens.",
journal = "Microbial Genomics",
publisher = "Microbiology Society",
volume = 3,
number = 7,
pages = "e000113",
month = jul,
year = 2017,
keywords = "MRSA; antimicrobial Resistance; hospital
network;Staphylococcus;Teaching antibiotic resistance
genomics;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Kumar2017-ri,
title = "Tuning of the Lethal Response to Multiple Stressors with a
{Single-Site} Mutation during Clinical Infection by
Staphylococcus aureus",
author = "Kumar, Krishan and Chen, John and Drlica, Karl and Shopsin, Bo",
abstract = "The agr system of Staphylococcus aureus promotes invasion of host
tissues, and as expected, agents that block agr quorum sensing
have anti-infective properties. Paradoxically, agr-defective
mutants are frequently recovered from patients, especially those
persistently infected with S. aureus. We found that an agr
deficiency increased survival of cultured bacteria during severe
stress, such as treatment with gentamicin, ciprofloxacin, heat,
or low pH. With daptomycin, deletion of agr decreased survival.
Therefore, agr activity can be either detrimental or protective,
depending on the type of lethal stress. Deletion of agr had no
effect on the ability of the antimicrobials to block bacterial
growth, indicating that agr effects are limited to lethal action.
Thus, the effect of an agr deletion is on bacterial tolerance,
not resistance. For gentamicin and daptomycin, activity can be
altered by agr-regulated secreted factors. For ciprofloxacin, a
detrimental function was downregulation of glutathione peroxidase
(bsaA), an enzyme responsible for defense against oxidative
stress. Deficiencies in agr and bsaA were epistatic for survival,
consistent with agr having a destructive role mediated by
reactive oxygen species. Enhanced susceptibility to lethal stress
by wild-type agr, particularly antimicrobial stress, helps
explain why inactivating mutations in S. aureus agr commonly
occur in hospitalized patients during infection. Moreover, the
agr quorum-sensing system of S. aureus provides a clinically
relevant example in which a single-step change in the response to
severe stress alters the evolutionary path of a pathogen during
infection.IMPORTANCE When phenotypes produced in response to an
environmental stress are inadequate to buffer against that
stress, changes that do buffer may become genetically encoded by
natural selection. A clinically relevant example is seen with S.
aureus mutants that are deficient in the key virulence regulator
agr. Paradoxically, defects in agr are selected during serious
hospital infection and have been associated with worse outcome.
The current work helps resolve this paradox: agr mutants are
often less readily killed by lethal stressors without affecting
MIC, a phenomenon known as tolerance. Our results indicate that
tolerance, which would not be detected as resistance, can be
selected in clinical settings. The data also support the ideas
that (i) S. aureus broadly hedges against environmental change
and stress through genome plasticity, (ii) reactive oxygen can be
involved in the self-destructive response in bacteria, and (iii)
therapeutic targeting of agr and virulence can be
counterproductive.",
journal = "MBio",
volume = 8,
number = 5,
month = nov,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Hau2017-di,
title = "Draft Genome Sequences of One {Methicillin-Sensitive} and Seven
{Methicillin-Resistant} \textit{Staphylococcus aureus} Sequence
Type 5 Isolates Obtained in California",
author = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and
Nicholson, Tracy L",
abstract = "Staphylococcus aureus is a commensal bacterium of humans that can
cause a spectrum of diseases. An isolate's capacity to cause
disease is partially attributed to the acquisition of novel
mobile genetic elements. This report provides the draft genome
sequence of one methicillin-susceptible and seven
methicillin-resistant clinical human S. aureus isolates.",
journal = "Genome Announc.",
volume = 5,
number = 42,
month = oct,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Lepuschitz2017-oz,
title = "Draft Genome Sequence of a {Community-Acquired}
{Methicillin-Resistant} \textit{Staphylococcus aureus} {USA300}
Isolate from a River Sample",
author = "Lepuschitz, Sarah and Mach, Robert and Springer, Burkhard and
Allerberger, Franz and Ruppitsch, Werner",
abstract = "The increasing emergence of multiresistant bacteria in health
care settings in the community and in the environment represents
a major health threat worldwide. Here, we report the draft genome
sequence of a community-acquired methicillin-resistant
Staphylococcus aureus (CA-MRSA) USA300 isolate (W1) from a small
river in southern Austria.",
journal = "Genome Announc.",
volume = 5,
number = 42,
month = oct,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Nemet2017-kj,
title = "Draft Genome Sequence of an Atypical Highly Virulent Rabbit
\textit{Staphylococcus aureus} Strain",
author = "N{\'e}met, Zolt{\'a}n and Albert, Ervin and Nagy, Tibor and
Olasz, Ferenc and Barta, Endre and Kiss, J{\'a}nos and D{\'a}n,
{\'A}d{\'a}m and B{\'a}nyai, Kriszti{\'a}n and Hermans, Katleen
and Biksi, Imre",
abstract = "Rabbit staphylococcosis is one of the most important diseases in
industrial rabbit production. We report here the draft genome
sequence of Staphylococcus aureus strain 380/11, an atypical
highly virulent (aHV) rabbit Staphylococcus aureus strain.",
journal = "Genome Announc.",
volume = 5,
number = 42,
month = oct,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Mohamed2017-ly,
title = "First Complete Genome Sequence of {Methicillin-Resistant}
\textit{Staphylococcus aureus} Strain {SO-1977} Isolated from
Khartoum, Sudan",
author = "Mohamed, Sofia B and Ali, Mohamed S and Alamir, Faisal M and
Alyas, Tahani B and Ahmed, Abdallah E and Seed, Almeen O and
Omer, Rihab A",
abstract = "Methicillin-resistant Staphylococcus aureus is increasingly
becoming resistant to most antibiotics and consequently has
become a challenging public health problem in Sudan. The present
study documented the first complete genome sequence of strain
SO-1977, isolated from a contaminated wound in Sudan.",
journal = "Genome Announc.",
volume = 5,
number = 42,
month = oct,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Senok2017-ku,
title = "Investigating a rare methicillin-resistant \textit{Staphylococcus
aureus} strain: first description of genome sequencing and
molecular characterization of {CC15-MRSA}",
author = "Senok, Abiola C and Somily, Ali M and Slickers, Peter and Raji,
Muhabat A and Garaween, Ghada and Shibl, Atef and Monecke, Stefan
and Ehricht, Ralf",
abstract = "PURPOSE: Methicillin resistant Staphylococcus aureus CC15 strains
(CC15-MRSA) have only been sporadically described in literature.
This study was carried out to describe the genetic make-up for
this rare MRSA strain. METHODS: Four CC15-MRSA isolates collected
in Riyadh, Saudi Arabia, between 2013 and 2014 were studied. Two
isolates were from clinical infection and 2 from retail meat
products. Whole genome sequencing was carried out using Illumina
HiSeq2500 genome analyzer. RESULTS: All the CC15-MRSA isolates
had the multilocus sequence typing profile ST1535,
13-13-1-1-81-11-13, which is a single locus variant of ST15. Of
the 6 contigs related to the SCC element, one comprised a
recombinase gene ccrAA, ccrC-PM1, fusC and a helicase, another
one included mvaS, dru, mecA and 1 had yobV and Q4LAG7. The SCC
element had 5 transposase genes, namely 3 identical paralogs of
tnpIS431 and 2 identical paralogs of tnpIS256. Two identical
copies of a tnpIS256-based insertion element flank the aacA-aphD
gene. Two copies of this insertion element were present with 1
located in the SCC element and another inserted into the sasC
gene. A short 3 kb region, which lacks any bacteriophage
structural genes and site-specific DNA integrase, was inserted
into the hlb gene. The hsdM and the 5'-part of the hsdS gene are
replaced by a copy of the hsdM/hsdS paralogs from $\nu$Sa$\beta$
giving rise to a new chimeric paralog of hsdS in $\nu$Sa$\alpha$.
CONCLUSION: CC15-MRSA shows a novel SCCmecV/SCCfus composite
element. Its variant of hsdM/hsdS probably facilitated uptake of
foreign mobile genetic elements that promoted emergence of
CC15-MRSA. Close surveillance is needed to monitor spread and
emergence of further CC15 MRSA strains.",
journal = "Infect. Drug Resist.",
volume = 10,
pages = "307--315",
month = oct,
year = 2017,
keywords = "MLST; MRSA; SCCmec; Saudi Arabia; clonal complex; whole genome
sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Kanjilal2017-dv,
title = "Trends in antibiotic susceptibility in Staphylococcus aureus in
Boston, Massachusetts, 2000-2014",
author = "Kanjilal, Sanjat and Sater, Mohamad R Abdul and Thayer, Maile and
Lagoudas, Georgia K and Kim, Soohong and Blainey, Paul C and
Grad, Yonatan H",
abstract = "The rate of infection by methicillin-resistant S. aureus (MRSA)
has declined over the past decade, but it is unclear whether this
represents a decline in S. aureus infections overall. To evaluate
trends in the annual rates of infection by S. aureus subtype and
mean antibiotic resistance, we conducted a 15-year retrospective
observational study at two tertiary care institutions in Boston,
MA of 31 753 adult inpatients with S. aureus isolated from
clinical specimens. We inferred gain and loss of methicillin
resistance through genome sequencing of 180 isolates from 2016.
Annual rates of infection by S. aureus declined from 2003 to 2014
by 4.2\% (2.7\%-5.6\%), attributable to an annual decline in MRSA
of 10.9\% (9.3\%-12.6\%). Penicillin-susceptible S. aureus (PSSA)
increased by 6.1\% (4.2\%-8.1\%) annually and rates of
methicillin-susceptible, penicillin-resistant S. aureus (MSSA)
did not change. Resistance in S. aureus decreased from 2000 to
2014 by 0.8 antibiotics (0.7-0.8). Within common MRSA clonal
complexes, 3/14 MSSA and 2/21 PSSA isolates arose from the loss
of resistance-conferring genes. Overall, in two tertiary care
institutions in Boston, MA, a decline in S. aureus infections has
been accompanied by a shift towards increased antibiotic
susceptibility. The rise in PSSA makes penicillin an increasingly
viable treatment option.",
journal = "J. Clin. Microbiol.",
month = nov,
year = 2017,
keywords = "Staphylococcus;antibiotics;transmission-epidemiology;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Zhang2017-ar,
title = "Preliminary comparative genomics revealed pathogenic potential
and international spread of Staphylococcus argenteus",
author = "Zhang, Dao-Feng and Zhi, Xiao-Yang and Zhang, Jing and Paoli,
George C and Cui, Yan and Shi, Chunlei and Shi, Xianming",
abstract = "BACKGROUND: Staphylococcus argenteus and S. schweitzeri, were
recently proposed as novel species within S. aureus complex
(SAC). S. argenteus has been reported in many countries and can
threaten human health. S. schweitzeri has not been associated
with human infections, but has been isolated from non-human
primates. Questions regarding the evolution of pathogenicity of
these two species will remain elusive until an exploratory
evolutionary framework is established. RESULTS: We present
genomic comparison analysis among members of SAC based on a
pan-genome definition, which included 15 S. argenteus genomes
(five newly sequenced), six S. schweitzeri genomes and 30
divergent S. aureus genomes. The three species had divergent core
genomes and rare interspecific recombination was observed among
the core genes. However, some subtypes of staphylococcal cassette
chromosome mec (SCCmec) elements and prophages were present in
different species. Of 111 tested virulence genes of S. aureus, 85
and 86 homologous genes were found in S. argenteus and S.
schweitzeri, respectively. There was no difference in virulence
gene content among the three species, but the sequence of most
core virulence genes was divergent. Analysis of the agr locus and
the genes in the capsular polysaccharides biosynthetic operon
revealed that they both diverged before the speciation of SAC
members. Furthermore, the widespread geographic distribution of
S. argenteus, sequence type 2250, showed ambiguous
biogeographical structure among geographically isolated
populations, demonstrating an international spread of this
pathogen. CONCLUSIONS: S. argenteus has spread among several
countries, and invasive infections and persistent carriage may be
not limited to currently reported regions. S. argenteus probably
had undergone a recent host adaption and can cause human
infections with a similar pathogenic potential.",
journal = "BMC Genomics",
volume = 18,
number = 1,
pages = "808",
month = oct,
year = 2017,
keywords = "Agr; Biogeographical structure; Capsular polysaccharides;
Comparative genomics; Staphylococcus argenteus; Staphylococcus
aureus; Staphylococcus schweitzeri; Virulence
gene;Staphylococcus;confirmed\_SA-resistance-mutation;pangenome;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Amissah2017-yh,
title = "Methicillin Resistant \textit{Staphylococcus aureus} Transmission
in a Ghanaian Burn Unit: The Importance of Active Surveillance in
{Resource-Limited} Settings",
author = "Amissah, Nana Ama and Buultjens, Andrew H and Ablordey, Anthony
and van Dam, Lieke and Opoku-Ware, Ampomah and Baines, Sarah L
and Bulach, Dieter and Tetteh, Caitlin S and Prah, Isaac and van
der Werf, Tjip S and Friedrich, Alexander W and Seemann, Torsten
and van Dijl, Jan Maarten and Stienstra, Ymkje and Stinear,
Timothy P and Rossen, John W",
abstract = "Objectives:Staphylococcus aureus infections in burn patients can
lead to serious complications and death. The frequency of S.
aureus infection is high in low- and middle-income countries
presumably due to limited resources, misuse of antibiotics and
poor infection control. The objective of the present study was to
apply population genomics to precisely define, for the first
time, the transmission of antibiotic resistant S. aureus in a
resource-limited setting in sub-Saharan Africa.
Methods:Staphylococcus aureus surveillance was performed amongst
burn patients and healthcare workers during a 7-months survey
within the burn unit of the Korle Bu Teaching Hospital in Ghana.
Results: Sixty-six S. aureus isolates (59 colonizing and 7
clinical) were obtained from 31 patients and 10 healthcare
workers. Twenty-one of these isolates were ST250-IV
methicillin-resistant S. aureus (MRSA). Notably, 25 (81\%) of the
31 patients carried or were infected with S. aureus within 24 h
of admission. Genome comparisons revealed six distinct S. aureus
clones circulating in the burn unit, and demonstrated multiple
transmission events between patients and healthcare workers.
Further, the collected S. aureus isolates exhibited a wide range
of genotypic resistances to antibiotics, including trimethoprim
(21\%), aminoglycosides (33\%), oxacillin (33\%), chloramphenicol
(50\%), tetracycline (59\%) and fluoroquinolones (100\%).
Conclusion: Population genomics uncovered multiple transmission
events of S. aureus, especially MRSA, within the investigated
burn unit. Our findings highlight lapses in infection control and
prevention, and underscore the great importance of active
surveillance to protect burn victims against multi-drug resistant
pathogens in resource-limited settings.",
journal = "Front. Microbiol.",
volume = 8,
pages = "1906",
month = oct,
year = 2017,
keywords = "Staphylococcus aureus; burn patients; comparative genomics;
healthcare workers; transmission
events;Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Coll2017-jb,
title = "Longitudinal genomic surveillance of {MRSA} in the {UK} reveals
transmission patterns in hospitals and the community",
author = "Coll, Francesc and Harrison, Ewan M and Toleman, Michelle S and
Reuter, Sandra and Raven, Kathy E and Blane, Beth and Palmer,
Beverley and Kappeler, A Ruth M and Brown, Nicholas M and
T{\"o}r{\"o}k, M Est{\'e}e and Parkhill, Julian and Peacock,
Sharon J",
abstract = "Genome sequencing has provided snapshots of the transmission of
methicillin-resistant Staphylococcus aureus (MRSA) during
suspected outbreaks in isolated hospital wards. Scale-up to
populations is now required to establish the full potential of
this technology for surveillance. We prospectively identified all
individuals over a 12-month period who had at least one
MRSA-positive sample processed by a routine diagnostic
microbiology laboratory in the East of England, which received
samples from three hospitals and 75 general practitioner (GP)
practices. We sequenced at least 1 MRSA isolate from 1465
individuals (2282 MRSA isolates) and recorded epidemiological
data. An integrated epidemiological and phylogenetic analysis
revealed 173 transmission clusters containing between 2 and 44
cases and involving 598 people (40.8\%). Of these, 118 clusters
(371 people) involved hospital contacts alone, 27 clusters (72
people) involved community contacts alone, and 28 clusters (157
people) had both types of contact. Community- and
hospital-associated MRSA lineages were equally capable of
transmission in the community, with instances of spread in
households, long-term care facilities, and GP practices. Our
study provides a comprehensive picture of MRSA transmission in a
sampled population of 1465 people and suggests the need to review
existing infection control policy and practice.",
journal = "Sci. Transl. Med.",
volume = 9,
number = 413,
month = oct,
year = 2017,
keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Wan2017-xr,
title = "Genomic comparison between Staphylococcus aureus {GN} strains
clinically isolated from a familial infection case: {IS1272}
transposition through a novel inverted repeat-replacing mechanism",
author = "Wan, Tsai-Wen and Higuchi, Wataru and Khokhlova, Olga E and Hung,
Wei-Chun and Iwao, Yasuhisa and Wakayama, Masataka and Inomata,
Noriyoshi and Takano, Tomomi and Lin, Yu-Tzu and Peryanova, Olga
V and Kojima, Kenji K and Salmina, Alla B and Teng, Lee-Jene and
Yamamoto, Tatsuo",
abstract = "A bacterial insertion sequence (IS) is a mobile DNA sequence
carrying only the transposase gene (tnp) that acts as a mutator
to disrupt genes, alter gene expressions, and cause genomic
rearrangements. ``Canonical'' ISs have historically been
characterized by their terminal inverted repeats (IRs), which may
form a stem-loop structure, and duplications of a short (non-IR)
target sequence at both ends, called target site duplications
(TSDs). The IS distributions and virulence potentials of
Staphylococcus aureus genomes in familial infection cases are
unclear. Here, we determined the complete circular genome
sequences of familial strains from a Panton-Valentine leukocidin
(PVL)-positive ST50/agr4 S. aureus (GN) infection of a 4-year old
boy with skin abscesses. The genomes of the patient strain (GN1)
and parent strain (GN3) were rich for ``canonical'' IS1272 with
terminal IRs, both having 13 commonly-existing copies
(ce-IS1272). Moreover, GN1 had a newly-inserted IS1272
(ni-IS1272) on the PVL-converting prophage, while GN3 had two
copies of ni-IS1272 within the DNA helicase gene and near rot.
The GN3 genome also had a small deletion. The targets of
ni-IS1272 transposition were IR structures, in contrast with
previous ``canonical'' ISs. There were no TSDs. Based on a
database search, the targets for ce-IS1272 were IRs or
``non-IRs''. IS1272 included a larger structure with tandem
duplications of the left (IRL) side sequence; tnp included minor
cases of a long fusion form and truncated form. One ce-IS1272 was
associated with the segments responsible for immune evasion and
drug resistance. Regarding virulence, GN1 expressed cytolytic
peptides (phenol-soluble modulin $\alpha$ and $\delta$-hemolysin)
and PVL more strongly than some other familial strains. These
results suggest that IS1272 transposes through an IR-replacing
mechanism, with an irreversible process unlike that of
``canonical'' transpositions, resulting in genomic variations,
and that, among the familial strains, the patient strain has
strong virulence potential based on community-associated
virulence factors.",
journal = "PLoS One",
volume = 12,
number = 11,
pages = "e0187288",
month = nov,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Stieber2017-ig,
title = "{PVL} overexpression due to genomic rearrangements and mutations
in the S. aureus reference strain {ATCC25923}",
author = "Stieber, Bettina and Sabat, Artur and Monecke, Stefan and
Slickers, Peter and Akkerboom, Viktoria and M{\"u}ller, Elke and
Friedrich, Alexander W and Ehricht, Ralf",
abstract = "OBJECTIVE: ATCC25923 is a Staphylococcus aureus strain that is
positive for the Panton Valentin leukocidin. It has been used for
decades as reference strain. We observed that two separately
maintained clones of ATCC25923 (``G477 and G478'') differed
grossly in the expression of this toxin. For that reason, both
clones were sequenced using an Illumina MiSeq instrument. After
assembling, the final sequences were analyzed and mapped to a
previously published ATCC25923 sequence (GenBank CP009361) using
bl2seq from the NCBI Blast2 package. RESULTS: The genomes of G477
and G478 size 2778,859 and 2792,213 nucleotides, respectively.
Both genomes include a circular plasmid of 27,490 nucleotides.
The sequence of the G477 chromosome maps nearly exactly to
CP009361. G478 has a slightly larger size because of the presence
of an additional transposable element tnp13k. The second copy of
that tnp13k element is located in an intergenic region between
the genes mazF and rsbU. The sequences of the ATCC25923 clones
G477 and G478 differ mainly in the insertion of a second tnp13k
element between the genes mazF and rsbU. That insertion may lead
to a different transcription of that genome region resulting in
upregulation of the expression of the Panton-Valentine leukocidin
in the ATCC25923 clone G478.",
journal = "BMC Res. Notes",
volume = 10,
number = 1,
pages = "576",
month = nov,
year = 2017,
keywords = "Panton-Valentine leukocidin (PVL); Protein expression; Sequence
mutation; Staphylococcus
aureus;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Takeuchi2016-jc,
title = "The Presence of Two {Receptor-Binding} Proteins Contributes to
the Wide Host Range of Staphylococcal {Twort-Like} Phages",
author = "Takeuchi, Ippei and Osada, Keita and Azam, Aa Haeruman and
Asakawa, Hiroaki and Miyanaga, Kazuhiko and Tanji, Yasunori",
abstract = "UNLABELLED: Thanks to their wide host range and virulence,
staphylococcal bacteriophages (phages) belonging to the genus
Twortlikevirus (staphylococcal Twort-like phages) are regarded as
ideal candidates for clinical application for Staphylococcus
aureus infections due to the emergence of antibiotic-resistant
bacteria of this species. To increase the usability of these
phages, it is necessary to understand the mechanism underlying
host recognition, especially the receptor-binding proteins (RBPs)
that determine host range. In this study, we found that the
staphylococcal Twort-like phage $\Phi$SA012 possesses at least
two RBPs. Genomic analysis of five mutant phages of $\Phi$SA012
revealed point mutations in orf103, in a region unique to
staphylococcal Twort-like phages. Phages harboring mutated ORF103
could not infect S. aureus strains in which wall teichoic acids
(WTAs) are glycosylated with $\alpha$-N-acetylglucosamine
($\alpha$-GlcNAc). A polyclonal antibody against ORF103 also
inhibited infection by $\Phi$SA012 in the presence of
$\alpha$-GlcNAc, suggesting that ORF103 binds to $\alpha$-GlcNAc.
In contrast, a polyclonal antibody against ORF105, a short tail
fiber component previously shown to be an RBP, inhibited phage
infection irrespective of the presence of $\alpha$-GlcNAc.
Immunoelectron microscopy indicated that ORF103 is a tail fiber
component localized at the bottom of the baseplate. From these
results, we conclude that ORF103 binds $\alpha$-GlcNAc in WTAs,
whereas ORF105, the primary RBP, is likely to bind the WTA
backbone. These findings provide insight into the infection
mechanism of staphylococcal Twort-like phages. IMPORTANCE:
Staphylococcus phages belonging to the genus Twortlikevirus
(called staphylococcal Twort-like phages) are considered
promising agents for control of Staphylococcus aureus due to
their wide host range and highly lytic capabilities. Although
staphylococcal Twort-like phages have been studied widely for
therapeutic purposes, the host recognition process of
staphylococcal Twort-like phages remains unclear. This work
provides new findings about the mechanisms of host recognition of
the staphylococcal Twort-like phage $\Phi$SA012. The details of
the host recognition mechanism of $\Phi$SA012 will allow us to
analyze the mechanisms of infection and expand the utility of
staphylococcal Twort-like phages for the control of S. aureus.",
journal = "Appl. Environ. Microbiol.",
volume = 82,
number = 19,
pages = "5763--5774",
month = oct,
year = 2016,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Sivaraman2017-ta,
title = "Draft Genome Sequence of a {Methicillin-Resistant} Sequence Type
39 Staphylococcal Isolate Obtained from Seafood",
author = "Sivaraman, G K and Vanik, Deesha and Visnuvinayagam, S and
Prasad, Mothadaka Mukteswar and Murugadas, V and Nadella, Ranjit
Kumar and Ravishankar, C N",
abstract = "The draft genome sequence of a methicillin-resistant
Staphylococcus aureus (MRSA) sequence type 39 (ST 39) isolate
obtained from the dried ribbonfish of Gujarat, India, is reported
here. Staphylococcus-specific genes were present in this MRSA
isolate. The whole-genome sequence of this strain contains 2,693
protein-coding genes and 70 RNAs within the 2.82-Mb genome.",
journal = "Genome Announc.",
volume = 5,
number = 45,
month = nov,
year = 2017,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Shylo_E_Wardyn2018-vx,
title = "{Whole-Genome} Analysis of Recurrent Staphylococcus aureus
{t571/ST398} Infection in Farmer, Iowa, {USA}",
author = "{Shylo E. Wardyn} and {Marc Stegger} and {Lance B. Price} and
{Tara C. Smith}",
abstract = "Staphylococcus aureus strain sequence type (ST) 398 has emerged
during the last decade, largely among persons who have contact
with swine or other livestock. Although colonization with ST398
is common in livestock workers, infections are not frequently
documented. We report recurrent ST398-IIa infection in an Iowa
farmer in contact with swine and cattle.",
journal = "Emerging Infectious Disease journal",
volume = 24,
number = 1,
year = 2018,
keywords = "antibiotic resistance; antimicrobial resistance; bacteria;
farmer; farming; Iowa; livestock; methicillin-resistant
Staphylococcus aureus; methicillin-sensitive S. aureus; MRSA;
MSSA; sequence types; swine; United States; whole-genome
analysis;
zoonosis;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
}
@ARTICLE{Lilje2017-hx,
title = "Whole-genome sequencing of bloodstream Staphylococcus aureus
isolates does not distinguish bacteraemia from endocarditis",
author = "Lilje, Berit and Rasmussen, Rasmus Vedby and Dahl, Anders and
Stegger, Marc and Skov, Robert Leo and Fowler, Vance G and Ng,
Kim Lee and Kiil, Kristoffer and Larsen, Anders Rhod and
Petersen, Andreas and Johansen, Helle Krogh and Sch{\o}nheyder,
Henrik Carl and Arpi, Magnus and Rosenvinge, Flemming S and
Korup, Eva and H{\o}st, Ulla and Hassager, Christian and Gill,
Sabine Ute Alice and Hansen, Thomas Fritz and Johannesen, Thor
Bech and Smit, Jesper and S{\o}gaard, Peter and Skytt Andersen,
Paal and Eske-Bruun, Niels",
abstract = "Most Staphylococcus aureus isolates can cause invasive disease
given the right circumstances, but it is unknown if some isolates
are more likely to cause severe infections than others. S. aureus
bloodstream isolates from 120 patients with definite infective
endocarditis and 121 with S. aureus bacteraemia without infective
endocarditis underwent whole-genome sequencing. Genome-wide
association analysis was performed using a variety of
bioinformatics approaches including SNP analysis, accessory
genome analysis and k-mer based analysis. Core and accessory
genome analyses found no association with either of the two
clinical groups. In this study, the genome sequences of S. aureus
bloodstream isolates did not discriminate between bacteraemia and
infective endocarditis. Based on our study and the current
literature, it is not convincing that a specific S. aureus
genotype is clearly associated to infective endocarditis in
patients with S. aureus bacteraemia.",
journal = "Microb Genom",
volume = 3,
number = 11,
month = nov,
year = 2017,
keywords = "Staphylococcus aureus; bacteraemia; genome-wide association;
infective
endocarditis;Staphylococcus;Staphylococcus\_aureus\_genome\_papers;GWAS-bacteria",
language = "en"
}
@ARTICLE{Carter2017-go,
title = "Topical antibiotic use co-selects for the carriage of mobile
genetic elements conferring resistance to unrelated
antimicrobials in \textit{Staphylococcus aureus}",
author = "Carter, Glen P and Schultz, Mark B and Baines, Sarah L and
Goncalves da Silva, Anders and Heffernan, Helen and Tiong, Audrey
and Pham, Peter H and Monk, Ian R and Stinear, Timothy P and
Howden, Benjamin P and Williamson, Deborah A",
abstract = "Topical antibiotics such as mupirocin and fusidic acid are
commonly used in the prevention and treatment of skin infections,
particularly those caused by staphylococci. However, widespread
use of these agents is associated with increased resistance to
these agents, potentially limiting their efficacy. Of particular
concern is the observation that resistance to topical antibiotics
is often associated with multidrug resistance, suggesting that
topical antibiotics may play a role in the emergence of
multidrug-resistant (MDR) strains.New Zealand (NZ) has some of
the highest globally recorded rates of topical antibiotic usage
and resistance. Using a combination of Pacific Biosciences Single
Molecule Real Time (SMRT) whole genome sequencing, Illumina short
read sequencing and Bayesian phylogenomic modelling on 118 new
multilocus sequence type 1 (ST1) community Staphylococcus aureus
isolates from New Zealand and 61 publically available
international ST1 genome sequences, we demonstrate a strong
correlation between the clinical introduction of topical
antibiotics and the emergence of MDR ST1 S. aureus We also
provide in vitro experimental evidence showing that exposure to
topical antibiotics can lead to the rapid selection of MDR S.
aureus isolates carrying plasmids that confer resistance to
multiple unrelated antibiotics, from within a mixed population of
competitor strains. These findings have important implications
regarding the impact of the indiscriminate use of topical
antibiotics.",
journal = "Antimicrob. Agents Chemother.",
month = dec,
year = 2017,
keywords = "Staphylococcus;antibiotics;chlorhexidine;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Chen2018-bt,
title = "Draft Genome Sequence of {USA100} {Methicillin-Resistant}
\textit{Staphylococcus aureus} Strain 209",
author = "Chen, Yingfeng and Crosby, Heidi A and Oosthuysen, 2nd, Wilhelm F
and Diekema, Daniel J and Kelley, Scott T and Horswill, Alexander
R",
abstract = "USA100 strains are significant contributors to the overall burden
of health care-associated methicillin-resistant Staphylococcus
aureus (MRSA) infections. Strain 209 is a representative MRSA
isolate that serves as a model organism for agr type II studies
and USA100 virulence assessments. We present a draft genome
sequence of this strain.",
journal = "Genome Announc.",
volume = 6,
number = 1,
month = jan,
year = 2018,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Challagundla2018-vw,
title = "Range Expansion and the Origin of {USA300} North American
Epidemic {Methicillin-Resistant} Staphylococcus aureus",
author = "Challagundla, Lavanya and Luo, Xiao and Tickler, Isabella A and
Didelot, Xavier and Coleman, David C and Shore, Anna C and
Coombs, Geoffrey W and Sordelli, Daniel O and Brown, Eric L and
Skov, Robert and Larsen, Anders Rhod and Reyes, Jinnethe and
Robledo, Iraida E and Vazquez, Guillermo J and Rivera, Raul and
Fey, Paul D and Stevenson, Kurt and Wang, Shu-Hua and Kreiswirth,
Barry N and Mediavilla, Jose R and Arias, Cesar A and Planet,
Paul J and Nolan, Rathel L and Tenover, Fred C and Goering,
Richard V and Robinson, D Ashley",
abstract = "The USA300 North American epidemic (USA300-NAE) clone of
methicillin-resistant Staphylococcus aureus has caused a wave of
severe skin and soft tissue infections in the United States since
it emerged in the early 2000s, but its geographic origin is
obscure. Here we use the population genomic signatures expected
from the serial founder effects of a geographic range expansion
to infer the origin of USA300-NAE and identify polymorphisms
associated with its spread. Genome sequences from 357 isolates
from 22 U.S. states and territories and seven other countries are
compared. We observe two significant signatures of range
expansion, including decreases in genetic diversity and increases
in derived allele frequency with geographic distance from the
Pennsylvania region. These signatures account for approximately
half of the core nucleotide variation of this clone, occur genome
wide, and are robust to heterogeneity in temporal sampling of
isolates, human population density, and recombination detection
methods. The potential for positive selection of a gyrA
fluoroquinolone resistance allele and several intergenic regions,
along with a 2.4 times higher recombination rate in a resistant
subclade, is noted. These results are the first to show a pattern
of genetic variation that is consistent with a range expansion of
an epidemic bacterial clone, and they highlight a rarely
considered but potentially common mechanism by which genetic
drift may profoundly influence bacterial genetic
variation.IMPORTANCE The process of geographic spread of an
origin population by a series of smaller populations can result
in distinctive patterns of genetic variation. We detect these
patterns for the first time with an epidemic bacterial clone and
use them to uncover the clone's geographic origin and variants
associated with its spread. We study the USA300 clone of
methicillin-resistant Staphylococcus aureus, which was first
noticed in the early 2000s and subsequently became the leading
cause of skin and soft tissue infections in the United States.
The eastern United States is the most likely origin of epidemic
USA300. Relatively few variants, which include an antibiotic
resistance mutation, have persisted during this clone's spread.
Our study suggests that an early chapter in the genetic history
of this epidemic bacterial clone was greatly influenced by random
subsampling of isolates during the clone's geographic spread.",
journal = "MBio",
volume = 9,
number = 1,
month = jan,
year = 2018,
keywords = "epidemics; fluoroquinolones; founder effects; genetic drift;
population genetics; range
expansion;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Delgado-Baquerizo2018-zw,
title = "A global atlas of the dominant bacteria found in soil",
author = "Delgado-Baquerizo, Manuel and Oliverio, Angela M and Brewer,
Tess E and Benavent-Gonz{\'a}lez, Alberto and Eldridge, David J
and Bardgett, Richard D and Maestre, Fernando T and Singh,
Brajesh K and Fierer, Noah",
abstract = "The immense diversity of soil bacterial communities has stymied
efforts to characterize individual taxa and document their
global distributions. We analyzed soils from 237 locations
across six continents and found that only 2\% of bacterial
phylotypes (~500 phylotypes) consistently accounted for almost
half of the soil bacterial communities worldwide. Despite the
overwhelming diversity of bacterial communities, relatively few
bacterial taxa are abundant in soils globally. We clustered
these dominant taxa into ecological groups to build the first
global atlas of soil bacterial taxa. Our study narrows down the
immense number of bacterial taxa to a ``most wanted'' list that
will be fruitful targets for genomic and cultivation-based
efforts aimed at improving our understanding of soil microbes
and their contributions to ecosystem functioning.",
journal = "Science",
publisher = "American Association for the Advancement of Science",
volume = 359,
number = 6373,
pages = "320--325",
month = jan,
year = 2018,
keywords = "microbiome;climate;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Becker2018-xs,
title = "{Plasmid-Encoded} Transferable {mecB-Mediated} Methicillin
Resistance in Staphylococcus aureus",
author = "Becker, Karsten and van Alen, Sarah and Idelevich, Evgeny A and
Schleimer, Nina and Seggewi{\ss}, Jochen and Mellmann, Alexander
and Kaspar, Ursula and Peters, Georg",
abstract = "During cefoxitin-based nasal screening, phenotypically
categorized methicillin-resistant Staphylococcus aureus (MRSA)
was isolated and tested negative for the presence of the mecA and
mecC genes as well as for the SCCmec-orfX junction region. The
isolate was found to carry a mecB gene previously described for
Macrococcus caseolyticus but not for staphylococcal species. The
gene is flanked by $\beta$-lactam regulatory genes similar to
mecR, mecI, and blaZ and is part of an 84.6-kb
multidrug-resistance plasmid that harbors genes encoding
additional resistances to aminoglycosides (aacA-aphD, aphA, and
aadK) as well as macrolides (ermB) and tetracyclines (tetS). This
further plasmidborne $\beta$-lactam resistance mechanism harbors
the putative risk of acceleration or reacceleration of MRSA
spread, resulting in broad ineffectiveness of $\beta$-lactams as
a main therapeutic application against staphylococcal infections.",
journal = "Emerg. Infect. Dis.",
volume = 24,
number = 2,
pages = "242--248",
month = feb,
year = 2018,
keywords = "MRSA; Macrococcus; Staphylococcaceae; Staphylococcus aureus;
antibacterial agents; antimicrobial resistance; bacteria; mecB;
methicillin-resistant Staphylococcus aureus; microbial genome;
plasmids;
staphylococci;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Ronco2018-qi,
title = "Genomic investigation of Staphylococcus aureus isolates from bulk
tank milk and dairy cows with clinical mastitis",
author = "Ronco, Troels and Klaas, Ilka C and Stegger, Marc and Svennesen,
Line and Astrup, L{\ae}rke B and Farre, Michael and Pedersen,
Karl",
abstract = "Staphylococcus aureus is one of the most common pathogens that
cause mastitis in dairy cows. Various subtypes, virulence genes
and mobile genetic elements have been associated with isolates
from bulk tank milk and clinical mastitis. So far, no Danish
cattle associated S. aureus isolates have been whole-genome
sequenced and further analyzed. Thus, the main objective was to
investigate the population structure and genomic content of
isolates from bulk tank milk and clinical mastitis, using
whole-genome sequencing. This may reveal the origin of strains
that cause clinical mastitis. S. aureus isolates from bulk tank
milk (n = 94) and clinical mastitis (n = 63) were collected from
91 and 24 different farms, respectively and whole-genome
sequenced. The genomic content was analyzed and a phylogenetic
tree based on single nucleotide polymorphisms was constructed. In
general, the isolates from both bulk tank milk and clinical
mastitis were of similar genetic background. This suggests that
dairy cows are natural carriers of the S. aureus subtypes that
cause clinical mastitis if the right conditions are present and
that a broad range of subtypes cause mastitis. A phylogenetic
cluster that mostly consisted of ST151 isolates carried three
mobile genetic elements that were primarily found in this group.
The prevalence of resistance genes was generally low. However,
the first ST398 methicillin resistant S. aureus isolate from a
Danish dairy cow with clinical mastitis was detected.",
journal = "Vet. Microbiol.",
volume = 215,
pages = "35--42",
month = feb,
year = 2018,
keywords = "Bulk tank milk; Clinical mastitis; Genomic analysis; S. aureus;
Virulence and resistance
genes;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Choe2018-me,
title = "Genome-scale analysis of Methicillin-resistant Staphylococcus
aureus {USA300} reveals a tradeoff between pathogenesis and drug
resistance",
author = "Choe, Donghui and Szubin, Richard and Dahesh, Samira and Cho,
Suhyung and Nizet, Victor and Palsson, Bernhard and Cho,
Byung-Kwan",
abstract = "Staphylococcus aureus infection is a rising public health care
threat. S. aureus is believed to have elaborate regulatory
networks that orchestrate its virulence. Despite its importance,
the systematic understanding of the transcriptional landscape of
S. aureus is limited. Here, we describe the primary transcriptome
landscape of an epidemic USA300 isolate of community-acquired
methicillin-resistant S. aureus. We experimentally determined
1,861 transcription start sites with their principal promoter
elements, including well-conserved -35 and -10 elements and
weakly conserved -16 element and 5' untranslated regions
containing AG-rich Shine-Dalgarno sequence. In addition, we
identified 225 genes whose transcription was initiated from
multiple transcription start sites, suggesting potential
regulatory functions at transcription level. Along with the
transcription unit architecture derived by integrating the
primary transcriptome analysis with operon prediction, the
measurement of differential gene expression revealed the
regulatory framework of the virulence regulator Agr, the
SarA-family transcriptional regulators, and $\beta$-lactam
resistance regulators. Interestingly, we observed a complex
interplay between virulence regulation, $\beta$-lactam
resistance, and metabolism, suggesting a possible tradeoff
between pathogenesis and drug resistance in the USA300 strain.
Our results provide platform resource for the location of
transcription initiation and an in-depth understanding of
transcriptional regulation of pathogenesis, virulence, and
antibiotic resistance in S. aureus.",
journal = "Sci. Rep.",
volume = 8,
number = 1,
pages = "2215",
month = feb,
year = 2018,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Suligoy2018-de,
title = "Mutation of Agr Is Associated with the Adaptation
ofStaphylococcus aureusto the Host during Chronic Osteomyelitis",
author = "Suligoy, Carlos M and Lattar, Santiago M and Noto Llana,
Mari{\'a}ngeles and Gonz{\'a}lez, Cintia D and Alvarez,
Luc{\'\i}a P and Robinson, D Ashley and G{\'o}mez, Marisa I and
Buzzola, Fernanda R and Sordelli, Daniel O",
abstract = "Selection pressures exerted onStaphylococcus aureusby host
factors may lead to the emergence of mutants better adapted to
the evolving conditions at the infection site. This study was
aimed at identifying the changes that occur inS. aureusexposed to
the host defense mechanisms during chronic osteomyelitis and
evaluating whether these changes affect the virulence of the
organism. Genome assessment of twoS. aureusisolates collected 13
months apart (HU-85a and HU-85c) from a host with chronic
osteomyelitis was made by whole genome sequencing. Agr
functionality was assessed by qRT-PCR. Isolates were tested in a
rat model of osteomyelitis and the bacterial load (CFU/tibia) and
the morphometric osteomyelitic index (OI) were determined. The
ability of the isolates to trigger the release of proinflammatory
cytokines was determined on macrophages in culture. Persistence
ofS. aureuswithin the host resulted in anagrCframeshift mutation
that likely led to the observed phenotype. The capacity to cause
bone tissue damage and trigger proinflammatory cytokines by
macrophages of theagr-deficient, unencapsulated derivative
(HU-85c) was decreased when compared with those of the isogenic
CP8-capsulated parental strain (HU-85a). By comparison, no
significant differences were found in the bacterial load or the
OI from rats challenged with isogenic Reynolds strains [CP5, CP8,
and non-typeable (NT)], indicating that lack of CP expression
alone was not likely responsible for the reduced capacity to
cause tissue damage in HU-85c compared with HU-85a. The
production of biofilm was significantly increased in the isogenic
derivative HU-85c. Lack ofagr-dependent factors makesS.
aureusless virulent during chronic osteomyelitis and alteration
of theagrfunctionality seems to permit better adaptation ofS.
aureusto the chronically infected host.",
journal = "Front. Cell. Infect. Microbiol.",
volume = 8,
pages = "18",
month = feb,
year = 2018,
keywords = "Staphylococcus aureus; adaptation; agr; biofilm; capsular
polysaccharide; chronic; infection;
osteomyelitis;Staphylococcus;host-pathogen;within-host-evolution;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Argemi2018-ot,
title = "Comparative Genomics and Identification of an
{Enterotoxin-Bearing} Pathogenicity Island, {SEPI-1/SECI-1}, in
Staphylococcus epidermidis Pathogenic Strains",
author = "Argemi, Xavier and Nanoukon, Chim{\`e}ne and Affolabi, Dissou and
Keller, Daniel and Hansmann, Yves and Riegel, Philippe and
Baba-Moussa, Lamine and Pr{\'e}vost, Gilles",
abstract = "Staphylococcus epidermidis is a leading cause of nosocomial
infections, majorly resistant to beta-lactam antibiotics, and may
transfer several mobile genetic elements among the members of its
own species, as well as toStaphylococcus aureus; however, a
genetic exchange fromS. aureustoS. epidermidisremains
controversial. We recently identified two pathogenic clinical
strains ofS. epidermidisthat produce a staphylococcal enterotoxin
C3-like (SEC) similar to that byS. aureuspathogenicity islands.
This study aimed to determine the genetic environment of the
SEC-coding sequence and to identify the mobile genetic elements.
Whole-genome sequencing and annotation of theS.
epidermidisstrains were performed using Illumina technology and a
bioinformatics pipeline for assembly, which provided evidence
that the SEC-coding sequences were located in a composite
pathogenicity island that was previously described in theS.
epidermidisstrain FRI909, called SePI-1/SeCI-1, with 83.8-89.7\%
nucleotide similarity. Various other plasmids were identified,
particularly p\_3\_95 and p\_4\_95, which carry antibiotic
resistance genes (hsrAanddfrG, respectively), and share
homologies with SAP085A and pUSA04-2-SUR11, two plasmids
described inS. aureus. Eventually, one complete prophage was
identified, $\Phi$SE90, sharing 30 out of 52 coding sequences
with theAcinetobacterphage vB\_AbaM\_IME200. Thus, the
SePI-1/SeCI-1 pathogenicity island was identified in two
pathogenic strains ofS. epidermidisthat produced a SEC
enterotoxin causing septic shock. These findings suggest the
existence of in vivo genetic exchange fromS. aureustoS.
epidermidis.",
journal = "Toxins",
volume = 10,
number = 3,
month = feb,
year = 2018,
keywords = "Staphylococcus aureus; Staphylococcus epidermidis; core genome;
enterotoxin; pan-genome; pathogenicity
island;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Kumburu2018-uw,
title = "Hospital Epidemiology of {Methicillin-ResistantStaphylococcus}
aureusin a Tertiary Care Hospital in Moshi, Tanzania, as
Determined by Whole Genome Sequencing",
author = "Kumburu, Happiness H and Sonda, Tolbert and Leekitcharoenphon,
Pimlapas and van Zwetselaar, Marco and Lukjancenko, Oksana and
Alifrangis, Michael and Lund, Ole and Mmbaga, Blandina T and
Kibiki, Gibson and Aarestrup, Frank M",
abstract = "Objective: To determine molecular epidemiology of
methicillin-resistantS. aureusin Tanzania using whole genome
sequencing. Methods: DNA from 33Staphylococcusspecies was
recovered from subcultured archivedStaphylococcusisolates. Whole
genome sequencing was performed on Illumina Miseq using
paired-end 2 $\times$ 250 bp protocol. Raw sequence data were
analyzed using online tools. Results: Full susceptibility to
vancomycin and chloramphenicol was observed. Thirteen isolates
(43.3\%) resisted cefoxitin and other antimicrobials tested.
Multilocus sequence typing revealed 13 different sequence types
among the 30S. aureusisolates, with ST-8 (n= seven, 23\%) being
the most common. Gene detection inS.aureusstains were as
follows:mecA, 10 (33.3\%);pvl, 5 (16.7\%);tst, 2 (6.7\%). The SNP
difference among the six Tanzanian ST-8 MRSA isolates ranged from
24 to 196 SNPs and from 16 to 446 SNPs when using the
USA300\_FPR3757 or the USA500\_2395 as a reference, respectively.
The mutation rate was 1.38 $\times$ 10-11SNPs/site/year or 1.4
$\times$ 10-6SNPs/site/year as estimated by USA300\_FPR3757 or
the USA500\_2395, respectively. Conclusion: S. aureus isolates
causing infections in hospitalized patients in Moshi are highly
diverse and epidemiologically unrelated. Temporal phylogenetic
analysis provided better resolution on transmission and
introduction of MRSA and it may be important to include this in
future routines.",
journal = "Biomed Res. Int.",
volume = 2018,
pages = "2087693",
month = jan,
year = 2018,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Bazaid2018-tp,
title = "Fatty Acid Supplementation Reverses the Small Colony Variant
Phenotype in {Triclosan-Adapted} Staphylococcus aureus: Genetic,
Proteomic and Phenotypic Analyses",
author = "Bazaid, Abdulrahman S and Forbes, Sarah and Humphreys, Gavin J
and Ledder, Ruth G and O'Cualain, Ronan and McBain, Andrew J",
abstract = "Staphylococcus aureus can develop a small colony variant (SCV)
phenotype in response to sub-lethal exposure to the biocide
triclosan. In the current study, whole genome sequencing was
performed and changes in virulence were investigated in five
Staphylococcus aureus strains following repeated exposure to
triclosan. Following exposure, 4/5 formed SCV and exhibited point
mutations in the triclosan target gene fabI with 2/4 SCVs showing
mutations in both fabI and fabD. The SCV phenotype was in all
cases immediately reversed by nutritional supplementation with
fatty acids or by repeated growth in the absence of triclosan,
although fabI mutations persisted in 3/4 reverted SCVs.
Virulence, determined using keratinocyte invasion and Galleria
mellonella pathogenicity assays was significantly (p < 0.05)
attenuated in 3/4 SCVs and in the non-SCV triclosan-adapted
bacterium. Proteomic analysis revealed elevated FabI in 2/3 SCV
and down-regulation in a protein associated with virulence in 1/3
SCV. In summary, attenuated keratinocyte invasion and larval
virulence in triclosan-induced SCVs was associated with decreases
in growth rate and virulence factor expression. Mutation occurred
in fabI, which encodes the main triclosan target in all SCVs and
the phenotype was reversed by fatty acid supplementation,
demonstrating an association between fatty acid metabolism and
triclosan-induced SCV.",
journal = "Sci. Rep.",
volume = 8,
number = 1,
pages = "3876",
month = mar,
year = 2018,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{You2018-er,
title = "Genomic differences between nasal Staphylococcus aureus from hog
slaughterhouse workers and their communities",
author = "You, Yaqi and Song, Li and Nonyane, Bareng A S and Price, Lance B
and Silbergeld, Ellen K",
abstract = "New human pathogens can emerge from the livestock-human interface
and spread into human populations through many pathways including
livestock products. Occupational contact with livestock is a risk
factor for exposure to those pathogens and may cause further
spreading of those pathogens in the community. The current study
used whole genome sequencing to explore nasal Staphylococcus
aureus obtained from hog slaughterhouse workers and their
community members, all of whom resided in a livestock-dense
region in rural North Carolina. Sequence data were analyzed for
lineage distribution, pathogenicity-related genomic features, and
mobile genetic elements. We observed evidence of nasal S. aureus
differences between hog workers and non-workers. Nasal S. aureus
from hog workers showed a greater lineage diversity than nasal S.
aureus from community residents. Hog worker isolates were less
likely to carry the $\varphi$Sa3 prophage and human-specific
immune evasion cluster genes than community resident isolates
($\varphi$Sa3 prophage: 54.5\% vs. 91.7\%, Benjamini-Hochberg
(BH) corrected p = 0.035; immune evasion cluster genes: 66.7\%
vs. 100\%, BH p = 0.021). Hog worker isolates had a lower
prevalence and diversity of enterotoxins than community resident
isolates, particularly lacking the enterotoxin gene cluster
(39.4\% vs. 70.8\%, BH p = 0.125). Moreover, hog worker isolates
harbored more diverse antibiotic resistance genes, with a higher
prevalence of carriage of multiple resistance genes, than
community resident isolates (75.8\% vs. 29.2\%, BH p = 0.021).
Phylogenetic analysis of all ST5 isolates, the most abundant
lineage in the collection, further supported separation of
isolates from hog workers and non-workers. Together, our
observations suggest impact of occupational contact with
livestock on nasal S. aureus colonization and highlight the need
for further research on the complex epidemiology of S. aureus at
the livestock-human interface.",
journal = "PLoS One",
volume = 13,
number = 3,
pages = "e0193820",
month = mar,
year = 2018,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Worthing2018-ee,
title = "Qac genes and biocide tolerance in clinical veterinary
methicillin-resistant and methicillin-susceptible Staphylococcus
aureus and Staphylococcus pseudintermedius",
author = "Worthing, Kate A and Marcus, Alan and Abraham, Sam and Trott,
Darren J and Norris, Jacqueline M",
abstract = "Qac genes are associated with increased tolerance to quaternary
ammonium compounds and other cationic biocides such as
chlorhexidine. This study aimed to determine whether qac genes
and increased biocide tolerance were present in 125 clinical
methicillin-resistant and susceptible veterinary staphylococci. A
total of 125 methicillin-resistant Staphylococcus aureus (MRSA)
and methicillin-resistant and -susceptible Staphylococcus
pseudintermedius (MRSP and MSSP) from three archived Australian
veterinary staphylococci collections underwent whole genome
sequencing, multilocus sequence typing and qac gene screening.
Two MRSA isolates (12\%) harboured qacA/B genes; both isolates
were ST8 from horses. QacJ, qacG and smr genes were identified in
28/90 (31\%) MRSP and 1/18 (6\%) MSSP isolates. ST71 MRSP was
significantly more likely to harbour qac genes than other MRSP
clones (p < 0.05). A random subset of 31 isolates underwent
minimum bactericidal concentration (MBC) testing against
F10SCTM(benzalkonium chloride and biguanide), and
HexaconTM(chlorhexidine gluconate), with and without the addition
of bovine serum albumin (BSA) as an in vitro substitute for
organic matter contamination. Qac genes were not associated with
increased phenotypic biocide tolerance but biocide efficacy was
significantly affected by the presence of BSA. In the absence of
BSA, all MBC values were well below the recommended usage
concentration. When BSA was present, regardless of qac gene
presence, 50\% of MRSA and 43\% of MRSP had an F10SCTMMBC above
the recommended concentration for general disinfection. Qac genes
did not confer increased in vitro biocide tolerance to veterinary
staphylococci. Organic matter contamination must be minimized to
ensure the efficacy of biocides against MRSA and MRSP.",
journal = "Vet. Microbiol.",
volume = 216,
pages = "153--158",
month = mar,
year = 2018,
keywords = "Biocide tolerance; Methicillin-resistance; Qac genes;
Staphylococcus; Veterinary;
Zoonosis;Staphylococcus;chlorhexidine;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Anson2018-he,
title = "{DNA} extraction from primary liquid blood cultures for
bloodstream infection diagnosis using whole genome sequencing",
author = "Anson, Luke W and Chau, Kevin and Sanderson, Nicholas and
Hoosdally, Sarah and Bradley, Phelim and Iqbal, Zamin and Phan,
Hang and Foster, Dona and Oakley, Sarah and Morgan, Marcus and
Peto, Tim E A and {Modernizing Medical Microbiology Informatics
Group Mmmig} and Crook, Derrick W and Pankhurst, Louise J",
abstract = "PURPOSE: Speed of bloodstream infection diagnosis is vital to
reduce morbidity and mortality. Whole genome sequencing (WGS)
performed directly from liquid blood culture could provide
single-assay species and antibiotic susceptibility prediction;
however, high inhibitor and human cell/DNA concentrations limit
pathogen recovery. We develop a method for the preparation of
bacterial DNA for WGS-based diagnostics direct from liquid blood
culture. METHODOLOGY: We evaluate three commercial DNA extraction
kits: BiOstic Bacteraemia, Amplex Hyplex and MolYsis Plus.
Differential centrifugation, filtration, selective lysis and
solid-phase reversible immobilization bead clean-up are tested to
improve human cells/DNA and inhibitor removal. Using WGS
(Illumina/MinION), we assess human DNA removal, pathogen
recovery, and predict species and antibiotic susceptibility
inpositive blood cultures of 44 Gram-negative and 54
Staphylococcus species.Results/Key findings. BiOstic kit
extractions yield the greatest mean DNA concentration, 94-301 ng
µl-1, versus 0-2.5 ng µl-1using Amplex and MolYsis kits. However,
we note higher levels of inhibition (260/280 ratio 0.9-2.1) and
human DNA (0.0-4.4$\times$106 copies) in BiOstic extracts.
Differential centrifugation (2000 g, 1 min) prior to BiOstic
extraction reduces human DNA by 63-89 \% with selective lysis
minimizing by a further 62 \%. Post-extraction bead clean-up
lowers inhibition. Overall, 67 \% of sequenced samples (Illumina
MiSeq) contain 93 \% concordance between WGS-based species and
susceptibility predictions and clinical diagnosis. If >60 \% of
sequencing reads are human (7/98 samples) susceptibility
prediction becomes compromised. Novel MinION-based WGS (n=9)
currently gives rapid species identification but not
susceptibility prediction. CONCLUSION: Our method for DNA
preparation allows WGS-based diagnosis direct from blood culture
bottles, providing species and antibiotic susceptibility
prediction in a single assay.",
journal = "J. Med. Microbiol.",
volume = 67,
number = 3,
pages = "347--357",
month = mar,
year = 2018,
keywords = "bacteraemia; bloodstream infection; sepsis; whole genome
sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
@ARTICLE{Purves2018-im,
title = "A horizontally gene transferred copper resistance locus confers
hyper-resistance to antibacterial copper toxicity and enables
survival of community acquired methicillin resistant
Staphylococcus aureus {USA300} in macrophages",
author = "Purves, Joanne and Thomas, Jamie and Riboldi, Gustavo Pelicoli
and Zapotoczna, Marta and Tarrant, Emma and Andrew, Peter W and
Londo{\~n}o, Alejandra and Planet, Paul J and Geoghegan, Joan A
and Waldron, Kevin J and Morrissey, Julie A",
abstract = "Excess copper is highly toxic and forms part of the host innate
immune system's antibacterial arsenal, accumulating at sites of
infection and acting within macrophages to kill engulfed
pathogens. We show for the first time that a novel, horizontally
gene transferred copper resistance locus (copXL), uniquely
associated with the SCCmec elements of the highly virulent,
epidemic, community acquired methicillin resistant Staphylococcus
aureus (CA-MRSA) USA300, confers copper hyper-resistance. These
genes are additional to existing core genome copper resistance
mechanisms, and are not found in typical S. aureus lineages, but
are increasingly identified in emerging pathogenic isolates. Our
data show that CopX, a putative P1B-3-ATPase efflux transporter,
and CopL, a novel lipoprotein, confer copper hyper-resistance
compared to typical S. aureus strains. The copXL genes form an
operon that is tightly repressed in low copper environments by
the copper regulator CsoR. Significantly, CopX and CopL are
important for S. aureus USA300 intracellular survival within
macrophages. Therefore the emergence of new S. aureus clones with
the copXL locus has significant implications for public health
because these genes confer increased resistance to antibacterial
copper toxicity, enhancing bacterial fitness by altering S.
aureus interaction with innate immunity. This article is
protected by copyright. All rights reserved.",
journal = "Environ. Microbiol.",
month = mar,
year = 2018,
keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
language = "en"
}
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