Zhou, Zhemin, McCann, Angela, Litrup, Eva, Murphy, Ronan, Cormican, Martin, Fanning, Seamus, Brown, Derek, Guttman, David S., Brisse, Sylvain and Achtman, Mark (2013) Neutral genomic microevolution of a recently emerged pathogen, salmonella enterica serovar agona. PLoS Genetics, 9 (4). e1003471. doi:10.1371/journal.pgen.1003471 ISSN 1553-7390.

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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.

Item Type:	Journal Article
Subjects:	Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics Q Science > QR Microbiology
Divisions:	Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Translational & Experimental Medicine
Library of Congress Subject Headings (LCSH):	Salmonella, Salmonella enterica, Salmonella -- Genetics, Bacterial genetics, Bacterial genomes
Journal or Publication Title:	PLoS Genetics
Publisher:	Public Library of Science
ISSN:	1553-7390
Official Date:	18 April 2013
Dates:	Date Event 18 April 2013 Published 7 March 2013 Accepted 10 January 2013 Submitted
Volume:	9
Number:	4
Article Number:	e1003471
DOI:	10.1371/journal.pgen.1003471
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Open Access (Creative Commons)
Date of first compliant deposit:	25 December 2015
Date of first compliant Open Access:	25 December 2015
Funder:	Science Foundation Ireland (SFI), Walton Fellowship (WF), Institut Pasteur (Paris, France), Institut de Veille Sanitaire (Saint Maurice, France) (INVS), France. Agence nationale de la recherche (ANR)
Grant number:	05/FE1/B882 (SFI) ; ANR-10-LABX-62-IBEID (ANR)

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