Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona

Zhemin Zhou*, Angela McCann, Eva Litrup, Ronan Murphy, Martin Cormican, Seamus Fanning, Derek Brown, David S. Guttman, Sylvain Brisse, Mark Achtman

*Corresponding author for this work

Research output: Contribution to journalArticle

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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. © 2013 Achtman et al

Original languageEnglish
Article number1003471
Pages (from-to)1-19
Number of pages19
JournalPLoS Genetics
Volume9
Issue number4
DOIs
Publication statusPublished - Apr 2013

Keywords

  • FIELD GEL-ELECTROPHORESIS
  • RESISTANT STAPHYLOCOCCUS-AUREUS
  • ESCHERICHIA-COLI O157
  • INTERNATIONAL OUTBREAK
  • YERSINIA-PESTIS
  • EVOLUTION
  • DIVERSITY
  • VIRULENCE
  • STRAINS
  • EPIDEMIOLOGY

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics
  • Cancer Research
  • Genetics(clinical)

Cite this

Zhou, Z., McCann, A., Litrup, E., Murphy, R., Cormican, M., Fanning, S., Brown, D., Guttman, D. S., Brisse, S., & Achtman, M. (2013). Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona. PLoS Genetics, 9(4), 1-19. [1003471]. https://doi.org/10.1371/journal.pgen.1003471