title: The ST131 Escherichia coli H22 subclone from human intestinal microbiota: Comparison of genomic and phenotypic traits with those of the globally successful H30 subclone.
abstract: In 2006, we found healthy subjects carrying ST131 Escherichia coli in their intestinal microbiota consisting of two populations: a subdominant population of fluoroquinolone-resistant E. coli belonging to subclone H30 (H30-R or subclade C1), the current worldwide dominant ST131 subclone, and a dominant E. coli population composed of antibiotic-susceptible E. coli belonging to subclone H22 (clade B), the precursor of subclone H30. We sequenced the whole genome of fecal H22 strain S250, compared it to the genomes of ExPEC ST131 H30-Rx strain JJ1886 and commensal ST131 H41 strain SE15, sought the H22-H30 genomic differences in our fecal strains and assessed their phenotypic consequences.
  
  
  
  We detected 173 genes found in the Virulence Factor Database, of which 148 were shared by the three ST131 genomes, whereas some were genome-specific, notably those allowing determination of virotype (D for S250 and C for JJ1886). We found three sequences of the FimH site involved in adhesion: two in S250 and SE15 close and identical, respectively, to that previously reported to confer strong intestinal adhesion, and one in JJ1886, corresponding to that commonly present in uropathogenic E. coli. Among the genes involved in sugar metabolism, one encoding a gluconate kinase lacked in S250 and JJ1886. Although this gene was also absent in both our fecal H22 and H30-R strains, H22 strains showed a higher capacity to grow in minimal medium with gluconate. Among the genes involved in gluconate metabolism, only the ghrB gene differed between S250/H22 and JJ1886/H30-R strains, resulting in different gluconate reductases. Of the genes involved in biofilm formation, two were absent in the three genomes and one, fimB, in the JJ1886 genome. Our fecal H30-R strains lacking intact fimB displayed delayed biofilm formation relative to our fecal H22 strains. The H22 strains differed by subclade B type and plasmid content, whereas the H30-R strains were identical.
  
  
  
  Phenotypic analysis of our fecal strains based on observed genomic differences between S250 and JJ1886 strains suggests the presence of traits related to bacterial commensalism in our H22 strains and traits commonly found in uropathogenic E. coli in our H30-R strains.
authors.affiliation: Service de Microbiologie, Hôpital Beaujon, AP-HP, Clichy, France. mhn.chanoine@aphp.fr.|Faculté de Médecine Paris Diderot, Paris, France. mhn.chanoine@aphp.fr.|INSERM UMR 1137, Université Paris 7, Paris, France. mhn.chanoine@aphp.fr.
authors.forename: Marie-Hélène
authors.initials: MH
authors.lastname: Nicolas-Chanoine
authors.affiliation: Laboratoire d'Hygiène Hospitalière, CHRU Besançon, Besançon, France.|UMR 6249 Chrono-Environnement, Besançon, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Petitjean
authors.affiliation: Laboratorio de Referencia de E. coli (LREC), Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain.
authors.forename: Azucena
authors.initials: A
authors.lastname: Mora
authors.affiliation: Service de Microbiologie, Hôpital Beaujon, AP-HP, Clichy, France.
authors.forename: Noémie
authors.initials: N
authors.lastname: Mayer
authors.affiliation: Institut National de la Santé et de la Recherche Médicale, U1047, Université de Montpellier, UFR de Médecine, Nîmes, France.|Service de Microbiologie, CHU Carémeau, Nîmes, France.
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Lavigne
authors.affiliation: Laboratoire d'Analyse Médicale du Centre, Coulommiers, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Boulet
authors.affiliation: Service de Microbiologie, Hôpital Beaujon, AP-HP, Clichy, France.
authors.forename: Véronique
authors.initials: V
authors.lastname: Leflon-Guibout
authors.affiliation: Laboratorio de Referencia de E. coli (LREC), Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain.
authors.forename: Jorge
authors.initials: J
authors.lastname: Blanco
authors.affiliation: Laboratoire d'Hygiène Hospitalière, CHRU Besançon, Besançon, France.|UMR 6249 Chrono-Environnement, Besançon, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Hocquet
mesh_terms: D018830:Adhesins, Escherichia coli / Q000235:genetics; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001422:Bacterial Adhesion / Q000235:genetics; D018441:Biofilms / Q000254:growth & development; D002244:Carbon / Q000378:metabolism; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins / Q000235:genetics; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D004927:Escherichia coli Infections / Q000382:microbiology; D029968:Escherichia coli Proteins / Q000235:genetics; D000072282:Extraintestinal Pathogenic Escherichia coli / Q000145:classification / Q000187:drug effects / Q000235:genetics; D005243:Feces / Q000382:microbiology; D036781:Fimbriae Proteins / Q000235:genetics; D024841:Fluoroquinolones / Q000494:pharmacology; D000069196:Gastrointestinal Microbiome; D005784:Gene Amplification; D005798:Genes, Bacterial / Q000235:genetics; D023281:Genomics; D005838:Genotype; D005942:Gluconates / Q000378:metabolism; D006801:Humans; D019426:Integrases / Q000235:genetics; D008780:Methyltransferases / Q000235:genetics; D008826:Microbial Sensitivity Tests; D064427:Nutritive Sweeteners / Q000378:metabolism; D010641:Phenotype; D017853:Phosphotransferases (Alcohol Group Acceptor) / Q000235:genetics / Q000378:metabolism; D010957:Plasmids / Q000235:genetics; D017421:Sequence Analysis; D037521:Virulence Factors / Q000235:genetics*
chemical_list: D018830:Adhesins, Escherichia coli; D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D024841:Fluoroquinolones; D005942:Gluconates; D064427:Nutritive Sweeteners; D037521:Virulence Factors; C081956:fimB protein, E coli; C058769:fimH protein, E coli; D036781:Fimbriae Proteins; D002244:Carbon; D008780:Methyltransferases; D017853:Phosphotransferases (Alcohol Group Acceptor); C020578:gluconokinase; D019426:Integrases; C030691:gluconic acid
keywords: Biofilm; E. coli ST131; H22 genome; Mannose-binding FimH region; Plasmid replicons; Subclades B; Sugar metabolism