title: Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar.
abstract: Salmonella enterica serovar Typhimurium definitive type 2 (DT2) is host restricted to Columba livia (rock or feral pigeon) but is also closely related to S. Typhimurium isolates that circulate in livestock and cause a zoonosis characterized by gastroenteritis in humans. DT2 isolates formed a distinct phylogenetic cluster within S. Typhimurium based on whole-genome-sequence polymorphisms. Comparative genome analysis of DT2 94-213 and S. Typhimurium SL1344, DT104, and D23580 identified few differences in gene content with the exception of variations within prophages. However, DT2 94-213 harbored 22 pseudogenes that were intact in other closely related S. Typhimurium strains. We report a novel in silico approach to identify single amino acid substitutions in proteins that have a high probability of a functional impact. One polymorphism identified using this method, a single-residue deletion in the Tar protein, abrogated chemotaxis to aspartate in vitro. DT2 94-213 also exhibited an altered transcriptional profile in response to culture at 42°C compared to that of SL1344. Such differentially regulated genes included a number involved in flagellum biosynthesis and motility. IMPORTANCE Whereas Salmonella enterica serovar Typhimurium can infect a wide range of animal species, some variants within this serovar exhibit a more limited host range and altered disease potential. Phylogenetic analysis based on whole-genome sequences can identify lineages associated with specific virulence traits, including host adaptation. This study represents one of the first to link pathogen-specific genetic signatures, including coding capacity, genome degradation, and transcriptional responses to host adaptation within a Salmonella serovar. We performed comparative genome analysis of reference and pigeon-adapted definitive type 2 (DT2) S. Typhimurium isolates alongside phenotypic and transcriptome analyses, to identify genetic signatures linked to host adaptation within the DT2 lineage.
authors: The Wellcome Trust Sanger Institute, the Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. rak@sanger.ac.uk
authors: Robert A
authors: RA
authors: Kingsley
authors: Sally
authors: S
authors: Kay
authors: Thomas
authors: T
authors: Connor
authors: Lars
authors: L
authors: Barquist
authors: Leanne
authors: L
authors: Sait
authors: Kathryn E
authors: KE
authors: Holt
authors: Karthi
authors: K
authors: Sivaraman
authors: Thomas
authors: T
authors: Wileman
authors: David
authors: D
authors: Goulding
authors: Simon
authors: S
authors: Clare
authors: Christine
authors: C
authors: Hale
authors: Aswin
authors: A
authors: Seshasayee
authors: Simon
authors: S
authors: Harris
authors: Nicholas R
authors: NR
authors: Thomson
authors: Paul
authors: P
authors: Gardner
authors: Wolfgang
authors: W
authors: Rabsch
authors: Paul
authors: P
authors: Wigley
authors: Tom
authors: T
authors: Humphrey
authors: Julian
authors: J
authors: Parkhill
authors: Gordon
authors: G
authors: Dougan
mesh_terms: D000222:Adaptation, Physiological; D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D010856:Columbidae; D016680:Genome, Bacterial; D058507:Host Specificity; D006801:Humans; D051379:Mice; D008810:Mice, Inbred C57BL; D008969:Molecular Sequence Data; D010802:Phylogeny; D012480:Salmonella Infections / Q000382:microbiology*; D012481:Salmonella Infections, Animal / Q000382:microbiology*; D012486:Salmonella typhimurium / Q000145:classification / Q000235:genetics / Q000472:pathogenicity / Q000502:physiology*; D059467:Transcriptome; D014774:Virulence
chemical_list: D001426:Bacterial Proteins
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