title: Genome-based Definition of an Inflammatory Bowel Disease-associated Adherent-Invasive Escherichia coli Pathovar.
abstract: BACKGROUND
  Mucosal-associated Escherichia coli are commonly found in inflamed tissues during inflammatory bowel disease (IBD). These bacteria often possess an adherent and invasive phenotype but lack virulence-associated features of well-described intestinal E. coli pathogens, and are of diverse serology and phylotypes, making it difficult to correlate strain characteristics with exacerbations of disease.
  
  
  METHODS
  The genome sequences of 14 phenotypically assigned adherent-invasive Escherichia coli (AIEC) isolates obtained from intestinal biopsies of patients with IBD were compared with the genome sequences of 37 other pathogenic and commensal E. coli available from public databases.
  
  
  RESULTS
  Core genome-based phylogenetic analyses and genome-wide comparison of genetic content established the existence of a closely related cluster of AIEC strains with 3 distinct genetic insertions differentiating them from commensal E. coli. These strains are of the B2 phylotype have a variant type VI secretion system (T6SS-1), and are highly related to extraintestinal pathogenic E. coli, suggesting that these 2 clinically distinct pathovars have common virulence strategies. Four other mucosally adherent E. coli strains from patients with IBD were of diverse phylogenetic origins and lacked the 3 genetic features, suggesting that they are not related to the B2 AIEC cluster. Although AIEC are often considered as having a unique association with Crohn's disease, isolates from Crohn's disease and ulcerative colitis were genetically indistinguishable.
  
  
  CONCLUSIONS
  B2 AIEC thus represent a closely related cluster of IBD-associated E. coli strains that are distinct from normal commensal isolates, and which should be considered separately from the phenotypically similar but genetically distinct non-B2 AIEC strains when considering their association with intestinal pathogenesis.
authors.affiliation: *Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; †Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; ‡Department of Microbiology, University of Manitoba; and §Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada.
authors.forename: Michael
authors.initials: M
authors.lastname: Desilets
authors.forename: Xianding
authors.initials: X
authors.lastname: Deng
authors.forename: Xiangding
authors.initials: X
authors.lastname: Deng
authors.forename: Chitong
authors.initials: C
authors.lastname: Rao
authors.forename: Alexander W
authors.initials: AW
authors.lastname: Ensminger
authors.forename: Denis O
authors.initials: DO
authors.lastname: Krause
authors.forename: Philip M
authors.initials: PM
authors.lastname: Sherman
authors.forename: Scott D
authors.initials: SD
authors.lastname: Gray-Owen
mesh_terms: D001422:Bacterial Adhesion / Q000235:genetics*; D004926:Escherichia coli / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity*; D004927:Escherichia coli Infections / Q000175:diagnosis / Q000382:microbiology*; D014644:Genetic Variation / Q000235:genetics*; D016680:Genome, Bacterial; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000175:diagnosis / Q000382:microbiology*; D010641:Phenotype; D010802:Phylogeny; D014774:Virulence