Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation


Autoři: Matt Bawn aff001;  Nabil-Fareed Alikhan aff001;  Gaëtan Thilliez aff001;  Mark Kirkwood aff001;  Nicole E. Wheeler aff003;  Liljana Petrovska aff004;  Timothy J. Dallman aff005;  Evelien M. Adriaenssens aff001;  Neil Hall aff002;  Robert A. Kingsley aff001
Působiště autorů: Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom aff001;  Earlham Institute, Norwich Research Park, Norwich, United Kingdom aff002;  Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Cambridge, United Kingdom aff003;  Animal and Plant Health Agency, Addlestone, United Kingdom aff004;  Gastrointestinal Bacteria Reference Unit, National Infection Service, Public Health England, London, United Kingdom aff005;  University of East Anglia, Norwich, United Kingdom aff006
Vyšlo v časopise: Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation. PLoS Genet 16(6): e32767. doi:10.1371/journal.pgen.1008850
Kategorie: Research Article
doi: 10.1371/journal.pgen.1008850

Souhrn

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 a minor phylogroup of ST36. The major phylogroup had a population structure with two high order clades (α and β) and multiple subclades on extended internal branches, that exhibited distinct signatures of host adaptation and anthropogenic selection. Clade α contained a number of subclades composed of strains from well characterized epidemics in domesticated animals, while clade β contained multiple subclades associated with wild avian species. The contrasting epidemiology of strains in clade α and β 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 α lineages from adaptation to circulation in populations of domesticated livestock, and the predisposition of clade β 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 α (SGI-1 and SGI-4).

Klíčová slova:

Antimicrobial resistance – Bacteriophages – Bird genomics – Livestock – Salmonella typhimurium – Sequence analysis – Sequence assembly tools – Sequence databases


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