Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona

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dc.contributor.author Zhou, Zhemin
dc.contributor.author McCann, Angela
dc.contributor.author Litrup, Eva
dc.contributor.author Murphy, Ronan
dc.contributor.author Cormican, Martin
dc.contributor.author Fanning, Séamus
dc.contributor.author Brown, Derek
dc.contributor.author Guttman, David S.
dc.contributor.author Brisse, Sylvain
dc.contributor.author Achtman, Mark
dc.date.accessioned 2016-02-17T11:46:19Z
dc.date.available 2016-02-17T11:46:19Z
dc.date.issued 2013
dc.identifier.citation Zhou Z, McCann A, Litrup E, Murphy R, Cormican M, Fanning S, et al. (2013) Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona. PLoS Genet 9(4): e1003471. doi:10.1371/journal.pgen.1003471 en
dc.identifier.volume 9 en
dc.identifier.issued 4 en
dc.identifier.issn 1553-7404
dc.identifier.uri http://hdl.handle.net/10468/2385
dc.identifier.doi 10.1371/journal.pgen.1003471
dc.description.abstract Salmonella enterica serovar Agona has caused multiple food-borne outbreaks of gastroenteritis since it was first isolated in 1952. We analyzed the genomes of 73 isolates from global sources, comparing five distinct outbreaks with sporadic infections as well as food contamination and the environment. Agona consists of three lineages with minimal mutational diversity: only 846 single nucleotide polymorphisms (SNPs) have accumulated in the non-repetitive, core genome since Agona evolved in 1932 and subsequently underwent a major population expansion in the 1960s. Homologous recombination with other serovars of S. enterica imported 42 recombinational tracts (360 kb) in 5/143 nodes within the genealogy, which resulted in 3,164 additional SNPs. In contrast to this paucity of genetic diversity, Agona is highly diverse according to pulsed-field gel electrophoresis (PFGE), which is used to assign isolates to outbreaks. PFGE diversity reflects a highly dynamic accessory genome associated with the gain or loss (indels) of 51 bacteriophages, 10 plasmids, and 6 integrative conjugational elements (ICE/IMEs), but did not correlate uniquely with outbreaks. Unlike the core genome, indels occurred repeatedly in independent nodes (homoplasies), resulting in inaccurate PFGE genealogies. The accessory genome contained only few cargo genes relevant to infection, other than antibiotic resistance. Thus, most of the genetic diversity within this recently emerged pathogen reflects changes in the accessory genome, or is due to recombination, but these changes seemed to reflect neutral processes rather than Darwinian selection. Each outbreak was caused by an independent clade, without universal, outbreak-associated genomic features, and none of the variable genes in the pan-genome seemed to be associated with an ability to cause outbreaks. en
dc.description.sponsorship Science Foundation Ireland (SFI Grant 05/FE1/B882) (SFI Walton Fellowship); Institut Pasteur, France; Institut de Veille Sanitaire, Saint-Maurice, France; Programme d'Investissements d'Avenir (PIA grant ANR-10-LABX-62-IBEID) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Public Library of Science en
dc.rights © 2013 Achtman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited en
dc.rights.uri http://creativecommons.org/licenses/by/4.0/ en
dc.subject Field gel electrophoresis en
dc.subject Resistant etaphylococcus aureus en
dc.subject Escherichia coli O157 en
dc.subject International outbreak en
dc.subject Yersinia pestis en
dc.subject Evolution en
dc.subject Diversity en
dc.subject Virulence en
dc.subject Strains en
dc.subject Epidemiology en
dc.title Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Angela McCann, Microbiology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: angela.mccann@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.internal.wokid WOS:000318073300064
dc.contributor.funder Science Foundation Ireland en
dc.contributor.funder Institut Pasteur en
dc.contributor.funder Programme d'Investissements d'Avenir, France
dc.contributor.funder Institut de Veille Sanitaire, Saint-Maurice, France
dc.description.status Peer reviewed en
dc.identifier.journaltitle PLOS GENETICS en
dc.internal.IRISemailaddress angela.mccann@ucc.ie en
dc.identifier.articleid e1003471


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© 2013 Achtman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Except where otherwise noted, this item's license is described as © 2013 Achtman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
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