Comparative genomics of adherent-invasive Escherichia coli (AIEC) associated with Crohn's disease. O-003.

Abstract

Intestinal bacteria are implicated increasingly as a pivotal factor in the development of Crohn's disease (CD) but the specific components of the complex polymicrobial environment driving the inflammatory response are unresolved. Using contemporary culture-independent methodologies we have discovered that the mucosal flora of people with Crohn's ileitis, Boxer dogs with granulomatous colitis, and mice with Toxoplasma and NSAID induced ileitis are selectively enriched in E. coli. Culture based characterization of E. coli from the inflamed mucosa of people, dogs and mice indicates they belong to a putative new pathogroup, Adherent and Invasive E. coli (AIEC), originally isolated from CD ileitis in France. Our findings raise the possibility that AIEC strains share common pathoadaptive determinants of virulence that promote intestinal inflammation across species. The overall objective of this study is to use comparative genomics to identify genes of AIEC strains that could provide novel insights into how these bacteria might elicit intestinal inflammation in a Crohn's susceptible individual. Roche/454 pyrosequencing, involving a combination of both single and paired-end reads from the FLX sequencer, was used to assemble the genome sequence of 7 AIEC strains (4 CD, 3 ileitis and 1 colitis; 1 murine ileitis; 2 granulomatous colitis of Boxer dogs) and one non-AIEC strain from CD ileum. The sequences were assembled into multicontig scaffolds ranging in number from 9-45 and with total genome sizes of 4.7-5.2 Mb. The sequences were compared to recently sequenced murine E. coli NC101 (induces IBD in IL10-/-mice) and publicly available genome sequences of E. coli and Shigella. E. fegusonii was used as an out group. Phylogenies based on the non-recombinant portion of the genome, involving over 600 loci, strongly supported the independent evolutionary history of AIEC strains, including AIEC from the same host and with the majority of AIEC closely related to different strains of extraintestinal pathogenic E. coli (ExPEC) e.g. UPEC and APEC. Based on gene content, AIEC as an overall pathotype did not cluster as a single group, rather AIEC strains from different species intermingled in several distinct clusters with ExPEC. Genomic comparisons across biochemical categories revealed that AIEC were overrepresented in siderophores, heme uptake, iron uptake, and biosynthesis of natural products compared to non-pathogenic strains. Compared to other E. coli pathogens AIEC were overrepresented in intracellular survival and replication, proinflamatory effects, and types II and IV secretory proteins, and lacking type III. We conclude that AIEC strains isolated from different host species have not descended from the same common ancestor and that overall they tend to be more closely related to ExPEC than to other E. coli. Our finding that the AIEC pathotype is overrepresented in genes related to iron utilization, intracellular survival and replication, and proinflamatory effects is highly relevant to its association with CD and provides guidance for subsequent functional analysis.