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

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.
Author Summary Pulsed-field gel electrophoresis (PFGE) is the gold standard for recognizing outbreaks of food-borne disease. Comparative genomics has been used to elucidate transmission chains and evolutionary patterns within bacterial pathogens. However, their global genetic diversity has not yet been compared across multiple food-borne outbreaks. It was uncertain whether such outbreaks are caused by closely related organisms or are due to genetic properties that were recently acquired by horizontal genetic transfer. We investigated Salmonella enterica serovar Agona, a common cause of food-borne gastroenteritis, by sequencing genomes from bacterial strains from five outbreaks, as well as sporadic disease and the environment. Each outbreak was caused by a genetically distinct variant, but closely related bacteria were also found in the environment or in animal sources. The erroneous identity of bacteria according to PFGE reflected repeated, neutral acquisitions of bacteriophages, and genetic acquisitions or losses were not uniform across outbreak strains. Our results indicate that genomic differences used by epidemiologists to reach important decisions for public health can be stochastic and unrelated to disease or fitness. Our results also define the population structure and minimal age of Agona, and suggest that many serovars of Salmonella may be of recent origin.