title: Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.
abstract: The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a widely disseminated zoonotic pathogen. Here, with an unprecedented national collection of isolates collected contemporaneously from humans and animals and including a sample of internationally derived isolates, we have used whole-genome sequencing to dissect the phylogenetic associations of the bacterium and its antimicrobial resistance genes through the course of an epidemic. Contrary to current tenets supporting a single homogeneous epidemic, we demonstrate that the bacterium and its resistance genes were largely maintained within animal and human populations separately and that there was limited transmission, in either direction. We also show considerable variation in the resistance profiles, in contrast to the largely stable bacterial core genome, which emphasizes the critical importance of integrated genotypic data sets in understanding the ecology of bacterial zoonoses and antimicrobial resistance.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
authors.forename: A E
authors.initials: AE
authors.lastname: Mather
authors.forename: S W J
authors.initials: SW
authors.lastname: Reid
authors.forename: D J
authors.initials: DJ
authors.lastname: Maskell
authors.forename: J
authors.initials: J
authors.lastname: Parkhill
authors.forename: M C
authors.initials: MC
authors.lastname: Fookes
authors.forename: S R
authors.initials: SR
authors.lastname: Harris
authors.forename: D J
authors.initials: DJ
authors.lastname: Brown
authors.forename: J E
authors.initials: JE
authors.lastname: Coia
authors.forename: M R
authors.initials: MR
authors.lastname: Mulvey
authors.forename: M W
authors.initials: MW
authors.lastname: Gilmour
authors.forename: L
authors.initials: L
authors.lastname: Petrovska
authors.forename: E
authors.initials: E
authors.lastname: de Pinna
authors.forename: M
authors.initials: M
authors.lastname: Kuroda
authors.forename: M
authors.initials: M
authors.lastname: Akiba
authors.forename: H
authors.initials: H
authors.lastname: Izumiya
authors.forename: T R
authors.initials: TR
authors.lastname: Connor
authors.forename: M A
authors.initials: MA
authors.lastname: Suchard
authors.forename: P
authors.initials: P
authors.lastname: Lemey
authors.forename: D J
authors.initials: DJ
authors.lastname: Mellor
authors.forename: D T
authors.initials: DT
authors.lastname: Haydon
authors.forename: N R
authors.initials: NR
authors.lastname: Thomson
mesh_terms: D000818:Animals; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D058872:Epidemics; D016680:Genome, Bacterial; D054884:Host-Pathogen Interactions; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012480:Salmonella Infections / Q000453:epidemiology / Q000382:microbiology*; D012481:Salmonella Infections, Animal / Q000453:epidemiology / Q000382:microbiology*; D012486:Salmonella typhimurium / Q000145:classification* / Q000187:drug effects / Q000235:genetics; D015047:Zoonoses / Q000382:microbiology*
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