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

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dc.contributor.authorZhou, Zhemin
dc.contributor.authorMcCann, Angela
dc.contributor.authorLitrup, Eva
dc.contributor.authorMurphy, Ronan
dc.contributor.authorCormican, Martin
dc.contributor.authorFanning, Séamus
dc.contributor.authorBrown, Derek
dc.contributor.authorGuttman, David S.
dc.contributor.authorBrisse, Sylvain
dc.contributor.authorAchtman, Mark
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderInstitut Pasteuren
dc.contributor.funderProgramme d'Investissements d'Avenir, France
dc.contributor.funderInstitut de Veille Sanitaire, Saint-Maurice, France
dc.date.accessioned2016-02-17T11:46:19Z
dc.date.available2016-02-17T11:46:19Z
dc.date.issued2013
dc.description.abstractSalmonella 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.sponsorshipScience 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.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleide1003471
dc.identifier.citationZhou 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.1003471en
dc.identifier.doi10.1371/journal.pgen.1003471
dc.identifier.issn1553-7404
dc.identifier.issued4en
dc.identifier.journaltitlePLOS GENETICSen
dc.identifier.urihttps://hdl.handle.net/10468/2385
dc.identifier.volume9en
dc.language.isoenen
dc.publisherPublic Library of Scienceen
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 crediteden
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectField gel electrophoresisen
dc.subjectResistant etaphylococcus aureusen
dc.subjectEscherichia coli O157en
dc.subjectInternational outbreaken
dc.subjectYersinia pestisen
dc.subjectEvolutionen
dc.subjectDiversityen
dc.subjectVirulenceen
dc.subjectStrainsen
dc.subjectEpidemiologyen
dc.titleNeutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agonaen
dc.typeArticle (peer-reviewed)en
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