1. Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation.
- Author
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Bawn, Matt, Alikhan, Nabil-Fareed, Thilliez, Gaëtan, Kirkwood, Mark, Wheeler, Nicole E., Petrovska, Liljana, Dallman, Timothy J., Adriaenssens, Evelien M., Hall, Neil, and Kingsley, Robert A.
- Subjects
SALMONELLA enterica serovar typhimurium ,SALMONELLA ,DRUG resistance in microorganisms ,SALMONELLA typhimurium ,GASTROENTERITIS ,SALMONELLA enterica ,VETERINARY epidemiology ,FOODBORNE diseases - Abstract
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 (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). Author summary: Salmonella Typhimurium is a leading cause of foodborne illness worldwide. Our current understanding of the biology of Salmonella is largely based on studies using just two laboratory strains of S. Typhimurium, with similar characteristics. Yet this pathogen exhibits a remarkable diversity in host range, outcome of infection, and risk to human health. To investigate the genetic basis of this diversity, we have explored the genetic relationship of a collection of isolates that represent a substantial portion of the diversity of S. Typhimurium, using whole genome sequencing. S. Typhimurium evolved forming two major groups that differ in their distribution in livestock and wild avian species. The livestock-associated group contained isolates commonly affecting human health and were often drug resistant, while the wild avian-associated group was rarely associated with drug resistance and less frequently associated with human infection. We report distinct evolutionary processes acting on subgroups of S. Typhimurium including loss of information content of genomes, and gain or loss of genes predicted to affect functions such as antimicrobial resistance, disease potential, and environmental survival, and functional diversification. This study provides a framework in which to understand the epidemiology of Salmonella and improve assessment of its risk to animal and human health. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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