title: Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica.
abstract: BACKGROUND
  Divergence of bacterial populations into distinct subpopulations is often the result of ecological isolation. While some studies have suggested the existence of Salmonella enterica subsp. enterica subclades, evidence for these subdivisions has been ambiguous. Here we used a comparative genomics approach to define the population structure of Salmonella enterica subsp. enterica, and identify clade-specific genes that may be the result of ecological specialization.
  
  
  RESULTS
  Multi-locus sequence analysis (MLSA) and single nucleotide polymorphisms (SNPs) data for 16 newly sequenced and 30 publicly available genomes showed an unambiguous subdivision of S. enterica subsp. enterica into at least two subpopulations, which we refer to as clade A and clade B. Clade B strains contain several clade-specific genes or operons, including a β-glucuronidase operon, a S-fimbrial operon, and cell surface related genes, which strongly suggests niche specialization of this subpopulation. An additional set of 123 isolates was assigned to clades A and B by using qPCR assays targeting subpopulation-specific SNPs and genes of interest. Among 98 serovars examined, approximately 20% belonged to clade B. All clade B isolates contained two pathogenicity related genomic islands, SPI-18 and a cytolethal distending toxin islet; a combination of these two islands was previously thought to be exclusive to serovars Typhi and Paratyphi A. Presence of β-glucuronidase in clade B isolates specifically suggests an adaptation of this clade to the vertebrate gastrointestinal environment.
  
  
  CONCLUSIONS
  S. enterica subsp. enterica consists of at least two subpopulations that differ specifically in genes involved in host and tissue tropism, utilization of host specific carbon and nitrogen sources and are therefore likely to differ in ecology and transmission characteristics.
authors.affiliation: Department of Food Science, Cornell University, Ithaca, NY 14853, USA. hcd5@cornell.edu
authors.forename: Henk C
authors.initials: HC
authors.lastname: den Bakker
authors.forename: Andrea I
authors.initials: AI
authors.lastname: Moreno Switt
authors.forename: Gregory
authors.initials: G
authors.lastname: Govoni
authors.forename: Craig A
authors.initials: CA
authors.lastname: Cummings
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Ranieri
authors.forename: Lovorka
authors.initials: L
authors.lastname: Degoricija
authors.forename: Karin
authors.initials: K
authors.lastname: Hoelzer
authors.forename: Lorraine D
authors.initials: LD
authors.lastname: Rodriguez-Rivera
authors.forename: Stephanie
authors.initials: S
authors.lastname: Brown
authors.forename: Elena
authors.initials: E
authors.lastname: Bolchacova
authors.forename: Manohar R
authors.initials: MR
authors.lastname: Furtado
authors.forename: Martin
authors.initials: M
authors.lastname: Wiedmann
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D015373:Bacterial Typing Techniques; D055028:Comparative Genomic Hybridization; D004269:DNA, Bacterial / Q000235:genetics; D005828:Genetics, Population; D016680:Genome, Bacterial; D044404:Genomic Islands; D058885:Multilocus Sequence Typing; D009876:Operon; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D019779:Salmonella enterica / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA; D037521:Virulence Factors / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial; D037521:Virulence Factors