title: Molecular diversity of Escherichia coli in the human gut: new ecological evidence supporting the role of adherent-invasive E. coli (AIEC) in Crohn's disease.
abstract: BACKGROUND
  Escherichia coli, particularly the adherent-invasive E. coli (AIEC) pathovar, has been increasingly implicated in the ethiopathogenesis of Crohn's disease (CD). We describe the richness, abundance, diversity, and pathogenic features of E. coli and AIEC strains that colonize the intestinal mucosa.
  
  
  METHODS
  Approximately 100 E. coli colonies per biopsy from 20 CD patients (18 biopsies from colon and 23 from ileum) and 28 healthy controls (C) (25, colon; 27, ileum) were isolated. Repetitive extragenic palindrome-polymerase chain reaction (Rep-PCR) and pulsed field gel electrophoresis (PFGE) were used to analyze the clonality of isolates. For AIEC identification, adhesion and invasion assays were performed over Intestine-407 cells, and the capacity to survive and replicate intracellularly was determined over macrophages J774. The serotypes, phylotypes, and genotypes (19 virulence genes) of strains were also investigated.
  
  
  RESULTS
  Mucosa-associated E. coli richness (E. coli subtypes/patient: C = 2.0 +/- 1.0; CD = 2.1 +/- 1.3) and diversity (Shannon Index: H'(C): 2.1 +/- 0.6; H'(CD): 2.5 +/- 0.8) were similar between CD and C, but higher E. coli counts were characteristic of CD patients (P = 0.010), particularly those with Crohn's ileitis (P = 0.001). Host-specific pulsotypes shared virulence features of ExPEC at similar frequencies between CD and C, except for iucD, which was more prevalent in E. coli from controls (C: 75%, CD: 40%, P = 0.027). In contrast, greater AIEC prevalence (% subjects with AIEC: CD = 51.9%; C = 16.7%; P = 0.003), abundance (% AIEC/E. coli: CD = 3.8 +/- 5.0%; C = 1.5 +/- 3.8%; P = 0.039), and richness (number of AIEC subtypes: CD = 0.8 +/- 1.4; C = 0.2 +/- 0.4; P = 0.015) of E. coli strains belonging to the AIEC pathovar was observed for CD patients. AIEC subtypes showed a high variability of seropathotypes and pulsotypes, although the B2 phylogroup was the most prevalent (AIEC: 64%, non-AIEC: 38%, P = 0.044).
  
  
  CONCLUSIONS
  New data about ecological parameters of AIEC reinforces the implication of AIEC in CD.
authors.affiliation: Departament de Biologia, Universitat de Girona, Girona, Spain. marga.martinez@udg.edu
authors.forename: Margarita
authors.initials: M
authors.lastname: Martinez-Medina
authors.forename: Xavier
authors.initials: X
authors.lastname: Aldeguer
authors.forename: Mireia
authors.initials: M
authors.lastname: Lopez-Siles
authors.forename: Ferran
authors.initials: F
authors.lastname: González-Huix
authors.forename: Carles
authors.initials: C
authors.lastname: López-Oliu
authors.forename: Ghizlane
authors.initials: G
authors.lastname: Dahbi
authors.forename: Jesus E
authors.initials: JE
authors.lastname: Blanco
authors.forename: Jorge
authors.initials: J
authors.lastname: Blanco
authors.forename: L Jesus
authors.initials: LJ
authors.lastname: Garcia-Gil
authors.forename: Arlette
authors.initials: A
authors.lastname: Darfeuille-Michaud
mesh_terms: D000328:Adult; D001422:Bacterial Adhesion; D001706:Biopsy; D002460:Cell Line; D003424:Crohn Disease / Q000453:epidemiology / Q000382:microbiology* / Q000473:pathology; D004847:Epithelial Cells / Q000166:cytology / Q000382:microbiology; D004926:Escherichia coli / Q000145:classification* / Q000235:genetics* / Q000472:pathogenicity; D004927:Escherichia coli Infections / Q000453:epidemiology / Q000382:microbiology* / Q000473:pathology; D005260:Female; D014644:Genetic Variation; D006801:Humans; D007079:Ileitis / Q000453:epidemiology / Q000382:microbiology / Q000473:pathology; D007413:Intestinal Mucosa / Q000382:microbiology* / Q000473:pathology; D008264:Macrophages / Q000166:cytology / Q000382:microbiology; D008297:Male; D008875:Middle Aged; D010641:Phenotype; D015995:Prevalence; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014774:Virulence; D055815:Young Adult