Evolution of MRSA During Hospital Transmission and Intercontinental Spread

Harris, Simon R.; Feil, Edward J.; Holden, Matthew T. G.; Quail, Michael A.; Nickerson, Emma K.; Chantratita, Narisara; Gardete, Susana; Tavares, Ana; Day, Nick; Lindsay, Jodi A.; Edgeworth, Jonathan D; Lencastre, Hermı́nia de; Parkhill, Julian; Peacock, Sharon J.; Bentley, Stephen D.

doi:10.1126/science.1182395

Cited by 1,002 publications

(1,117 citation statements)

References 26 publications

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“…To infer a temporal scale, we estimated the rate of nucleotide substitution using published whole-genome data from ST239, sampled over a 20-year period [7]. A rate estimate obtained from these data was used to inform a prior applying only to third codon positions.…”

Section: Methodsmentioning

confidence: 99%

“…To deal with the challenges of these data, we introduce two methodological innovations. First, to add a temporal scale to our phylogeny, we estimate rates of substitution from whole-genome sequences of S. aureus with known dates of isolation in the recent past [6][7][8]. We use these estimates to constrain rates at sites least likely to be affected by weak purifying selection (which can decrease rates over the longer term [9]), while also allowing for rate variation across the tree.…”

Section: Introductionmentioning

confidence: 99%

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Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication

et al. 2012

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).Host species switches by bacterial pathogens leading to new endemic infections are important evolutionary events that are difficult to reconstruct over the long term. We investigated the host switching of Staphylococcus aureus over a long evolutionary timeframe by developing Bayesian phylogenetic methods to account for uncertainty about past host associations and using estimates of evolutionary rates from serially sampled whole-genome data. Results suggest multiple jumps back and forth between human and bovids with the first switch from humans to bovids taking place around 5500 BP, coinciding with the expansion of cattle domestication throughout the Old World. The first switch to poultry is estimated at around 275 BP, long after domestication but still preceding large-scale commercial farming. These results are consistent with a central role for anthropogenic change in the emergence of new endemic diseases.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication

et al. 2012

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“…A small number of MRSA clones have dominated globally in hospital settings, and progressive waves of different clones have occurred over time. 8,9 Currently, sequence type (ST) 22 (EMRSA-15) has been growing in importance in the UK, Europe, South-East Asia (i.e. Singapore) and Australia, and is replacing other MRSA clones (ST36 or EMRSA-16 in the UK, ST239 in Singapore and Australia).…”

mentioning

confidence: 99%

Differing epidemiology of two major healthcare-associated meticillin-resistant Staphylococcus aureus clones

Jeremiah

Kandiah

Spelman

et al. 2016

Journal of Hospital Infection

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This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. M A N U S C R I P T A C C E P T E D ACCEPTED MANUSCRIPT

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“…Consequently, staphylococci have been subjected to many molecular epidemiology studies 80 , including WGS analyses [41][42][43][44][45][46]82 . Many areas of the biology and pathology of these organisms have been investigated, including their evolution (particularly the origins of MRSA) in hospitals and communities 83,84 , the spread of clones among animals and humans 85 , the dynamics of colonization and infection 86 , and outbreak detection and control 87 .…”

Section: Applying Gene-by-gene Analysismentioning

confidence: 99%

MLST revisited: the gene-by-gene approach to bacterial genomics

et al. 2013

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Multilocus sequence typing (MLST) was proposed in 1998 as a portable sequence-based method for identifying clonal relationships among bacteria. Today, in the whole-genome era of microbiology, the need for systematic, standardized descriptions of bacterial genotypic variation remains a priority. Here, to meet this need, we draw on the successes of MLST and 16S rRNA gene sequencing to propose a hierarchical gene-by-gene approach that reflects functional and evolutionary relationships and catalogues bacteria 'from domain to strain'. Our gene-based typing approach using online platforms such as the Bacterial Isolate Genome Sequence Database (BIGSdb) allows the scalable organization and analysis of whole-genome sequence data.Advances in nucleotide-sequencing technology have provided unparalleled access to the enormous genetic diversity that has accumulated in the bacterial domain during 3.5-4 billion years of evolution 1 . Numerous sets of whole-genome sequencing (WGS) data for bacterial isolates (BOX 1) are available 2 , and metagenomic studies using these technologies continue to reveal further, seemingly boundless, diversity in bacterial communities 3 . Faced with this plethora of information, microbiologists must develop structured means of describing this diversity and of linking phenotype and genotype, thereby facilitating an improved understanding of the microbiological world. Given that we have precise information on the function of only a very small proportion of bacterial genes, and no knowledge at all about most, this is a formidable, if extremely exciting, challenge.Here, we focus primarily on pathogenic bacteria, although the concepts discussed are applicable more widely to all bacteria and archaea. Bacterial pathogens played a crucial part in the development of experimental microbiology and remain the most intensively studied prokaryotes more than 100 years later 4 . Pathogens have emerged across the diversity of the bacterial -but, interestingly, not the archaeal -domain on many occasions and are both polyphyletic and highly diverse. Thus, although pathogens represent only a tiny subset of the bacterial world, the challenges faced by the clinical microbiology laboratory are representative of those faced by microbiology as a whole.Taxonomic and functional analyses are based on the observations that diversity among bacteria is not continuous and that distinct, stable types with particular properties exist 5 . These founding principles of microbiology 6 have been upheld by much subsequent research, but the study of such clusters remains largely descriptive, and the evolutionary mechanisms that led to cluster emergence and persistence remain incompletely understood 7,8 . Structuring is also evident within bacterial genomes, as diversity is unevenly distributed among genes Pre-WGS cataloguing of diversityA major advance in defining bacterial diversity was the proposal, by the late Carl Woese and colleagues, of a universal and 'natural' -that is, genealogical -classification system based on small-su...

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Evolution of MRSA During Hospital Transmission and Intercontinental Spread

Cited by 1,002 publications

References 26 publications

Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication

Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication

Differing epidemiology of two major healthcare-associated meticillin-resistant Staphylococcus aureus clones

MLST revisited: the gene-by-gene approach to bacterial genomics

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