Evolution of Salmonella enterica serotypeTyphimurium driven by anthropogenicselection and niche adaptation

Bawn M,Alikhan N,Thilliez G,Adriaenssens E,Hall N,Kingsley R. (2020)

PLoS Genetics

Salmonella enterica serotype Typhimurium (S. Typhimurium) is a leading cause of gastroenteritis
and bacteraemia worldwide, and a model organism for the study of host-pathogen
interactions. Two S. Typhimurium strains (SL1344 and ATCC14028) are widely used to
study host-pathogen interactions, yet genotypic variation results in strains with diverse host
range, pathogenicity and risk to food safety. The population structure of diverse strains of S.
Typhimurium revealed a major phylogroup of predominantly sequence type 19 (ST19) and
minor of ST36. The major phylogroup had a population structure with two high order clades
(a and ß) and multiple subclades on extended internal branches, that exhibited distinct signatures
of host adaptation and anthropogenic selection. Clade a contained a number of subclades
composed of strains from well characterized epidemics in domesticated animals,
while clade ß contained multiple subclades associated with wild avian species. The contrasting
epidemiology of strains in clade a and ß was reflected by the distinct distribution of antimicrobial
resistance (AMR) genes, accumulation of hypothetically disrupted coding
sequences (HDCS), and signatures of functional diversification. These observations were
consistent with elevated anthropogenic selection of clade a lineages from adaptation to circulation
in populations of domesticated livestock, and the predisposition of clade ß lineages
to undergo adaptation to an invasive lifestyle by a process of convergent evolution with of
host adapted Salmonella serotypes. Gene flux was predominantly driven by acquisition and
recombination of prophage and associated cargo genes, with only occasional loss of these
elements. The acquisition of large chromosomally-encoded genetic islands was limited, but
notably, a feature of two recent pandemic clones (DT104 and monophasic S. Typhimurium
ST34) of clade a (SGI-1 and SGI-4).

PLoS Genetics

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