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Here, whole-genome-sequencing-powered epidemiology linked horizontal transfer of a virulence gene, sopE<\/jats:italic>, to the emergence and clonal expansion of a new epidemic \n \n Salmonella enterica<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> serovar Typhimurium (S<\/jats:italic>. Typhimurium) clone. The sopE<\/jats:italic> gene is sporadically distributed within the genus \n \n Salmonella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> and rare in \n \n S<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>. \n \n enterica<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> Typhimurium lineages, but was acquired multiple times during clonal expansion of the currently dominant pandemic monophasic S<\/jats:italic>. Typhimurium sequence type (ST) 34 clone. Ancestral state reconstruction and time-scaled phylogenetic analysis indicated that sopE<\/jats:italic> was not present in the common ancestor of the epidemic clade, but later acquisition resulted in increased clonal expansion of sopE<\/jats:italic>-containing clones that was temporally associated with emergence of the epidemic, consistent with increased fitness. The sopE<\/jats:italic> gene was mainly associated with a temperate bacteriophage mTmV, but recombination with other bacteriophage and apparent horizontal gene transfer of the sopE<\/jats:italic> gene cassette resulted in distribution among at least four mobile genetic elements within the monophasic \n \n S<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>. \n \n enterica<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> Typhimurium ST34 epidemic clade. The mTmV prophage lysogenic transfer to other \n \n S. enterica<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> serovars in vitro<\/jats:italic> was limited, but included the common pig-associated \n \n S<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>. \n \n enterica<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> Derby (S<\/jats:italic>. Derby). This may explain mTmV in S<\/jats:italic>. Derby co-circulating on farms with monophasic S<\/jats:italic>. Typhimurium ST34, highlighting the potential for further transfer of the sopE<\/jats:italic> virulence gene in nature. We conclude that whole-genome epidemiology pinpoints potential drivers of evolutionary and epidemiological dynamics during pathogen emergence, and identifies targets for subsequent research in epidemiology and bacterial pathogenesis.<\/jats:p>","DOI":"10.1099\/mgen.0.000456","type":"journal-article","created":{"date-parts":[[2020,10,28]],"date-time":"2020-10-28T16:23:05Z","timestamp":1603902185000},"source":"Crossref","is-referenced-by-count":18,"title":["Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone"],"prefix":"10.1099","volume":"6","author":[{"given":"Eleonora","family":"Tassinari","sequence":"first","affiliation":[{"name":"Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland"},{"name":"Quadram Institute Bioscience, Norwich Research Park, Norwich, 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