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dc.contributor.authorJamrozy, Dorota M.
dc.contributor.authorHarris, Simon R.
dc.contributor.authorMohamed, Naglaa
dc.contributor.authorPeacock, Sharon J.
dc.contributor.authorTan, Charles Y.
dc.contributor.authorParkhill, Julian
dc.contributor.authorAnderson, Annaliesa S.
dc.contributor.authorHolden, Matthew T. G.
dc.date.accessioned2016-06-06T16:30:07Z
dc.date.available2016-06-06T16:30:07Z
dc.date.issued2016-05-31
dc.identifier.citationJamrozy , D M , Harris , S R , Mohamed , N , Peacock , S J , Tan , C Y , Parkhill , J , Anderson , A S & Holden , M T G 2016 , ' Pan-genomic perspective on the evolution of the Staphylococcus aureus USA300 epidemic ' , Microbial Genomics , vol. 2 , no. 5 , pp. 1-14 . https://doi.org/10.1099/mgen.0.000058en
dc.identifier.issn2057-5858
dc.identifier.otherPURE: 243159670
dc.identifier.otherPURE UUID: d7eca450-0580-487b-971c-7d9464fd48da
dc.identifier.otherBibtex: urn:adb9329645f65b6607794b26032b7cbe
dc.identifier.otherScopus: 85045976726
dc.identifier.otherORCID: /0000-0002-4958-2166/work/60196495
dc.identifier.otherWOS: 000431153700001
dc.identifier.urihttps://hdl.handle.net/10023/8941
dc.descriptionS. R. H. and J. P. were supported by Wellcome Trust grant 098051. This work was funded by Pfizer Vaccine Research and Development.en
dc.description.abstractStaphylococcus 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.
dc.format.extent14
dc.language.isoeng
dc.relation.ispartofMicrobial Genomicsen
dc.rights© 2016 The Authors. Published by the Microbiology Society. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/).en
dc.subjectMRSAen
dc.subjectUSA300en
dc.subjectEvolutionen
dc.subjectRA0421 Public health. Hygiene. Preventive Medicineen
dc.subjectNDASen
dc.subjectSDG 3 - Good Health and Well-beingen
dc.subject.lccRA0421en
dc.titlePan-genomic perspective on the evolution of the Staphylococcus aureus USA300 epidemicen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews. School of Medicineen
dc.contributor.institutionUniversity of St Andrews. Infection Groupen
dc.contributor.institutionUniversity of St Andrews. Biomedical Sciences Research Complexen
dc.identifier.doihttps://doi.org/10.1099/mgen.0.000058
dc.description.statusPeer revieweden


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