Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli

• Published in: Gut Vol. 66; no. 8; pp. 1382 - 1389
• Main Authors: O'Brien, Claire L, Bringer, Marie-Agnès, Holt, Kathryn E, Gordon, David M, Dubois, Anaëlle L, Barnich, Nicolas, Darfeuille-Michaud, Arlette, Pavli, Paul
• Format: Journal Article
• Language: English
• Published: England BMJ Publishing Group LTD 01.08.2017; BMJ Publishing Group
• Subjects: Bacteria; Bacterial Adhesion; Bacteriology; Biochemistry, Molecular Biology; Biopsy; Cell Line; Clustered Regularly Interspaced Short Palindromic Repeats; Colorectal cancer; CRISPR; Crohn Disease - microbiology; Crohn's disease; Cytokines - secretion; DNA, Bacterial - analysis; E coli; Epithelial Cells - microbiology; Escherichia coli; Escherichia coli - genetics; Escherichia coli - growth & development; Escherichia coli Infections - complications; Genome; Genomes; Genomics; Genotype & phenotype; Host-Pathogen Interactions; Human health and pathology; Humans; Hépatology and Gastroenterology; Inflammatory bowel disease; Interleukin-10 - secretion; Interleukin-6 - secretion; Interleukin-8 - secretion; Life Sciences; Macrophages - microbiology; Macrophages - secretion; Microbiology and Parasitology; Mutation; Nucleic acids; Phenotype; Phylogeny; Rodents; Sequence Analysis, DNA; Tumor Necrosis Factor-alpha - secretion; CROHN'S DISEASE; INTESTINAL MICROBIOLOGY; ENTERIC BACTERIAL MICROFLORA; intestinal microbiology; enteric bacterial microflora; Crohn's disease
• DOI: 10.1136/gutjnl-2015-311059
• ISSN: 0017-5749; 1468-3288

ObjectiveAdherent-invasive Escherichia coli (AIEC) are a leading candidate bacterial trigger for Crohn's disease (CD). The AIEC pathovar is defined by in vitro cell-line assays examining specific bacteria/cell interactions. No molecular marker exists for their identification. Our aim was to identify a molecular property common to the AIEC phenotype.Design41 B2 phylogroup E. coli strains were isolated from 36 Australian subjects: 19 patients with IBD and 17 without. Adherence/invasion assays were conducted using the I-407 epithelial cell line and survival/replication assays using the THP-1 macrophage cell line. Cytokine secretion tumour necrosis factor ((TNF)-α, interleukin (IL) 6, IL-8 and IL-10) was measured using ELISA. The genomes were assembled and annotated, and cluster analysis performed using CD-HIT. The resulting matrices were analysed to identify genes unique/more frequent in AIEC strains compared with non-AIEC strains. Base composition differences and clustered regularly interspaced palindromic repeat (CRISPR) analyses were conducted.ResultsOf all B2 phylogroup strains assessed, 79% could survive and replicate in macrophages. Among them, 11/41 strains (5 CD, 2 UCs, 5 non-IBD) also adhere to and invade epithelial cells, a phenotype assigning them to the AIEC pathovar. The AIEC strains were phylogenetically heterogeneous. We did not identify a gene (or nucleic acid base composition differences) common to all, or the majority of, AIEC. Cytokine secretion and CRISPRs were not associated with the AIEC phenotype.ConclusionsComparative genomic analysis of AIEC and non-AIEC strains did not identify a molecular property exclusive to the AIEC phenotype. We recommend a broader approach to the identification of the bacteria-host interactions that are important in the pathogenesis of Crohn's disease.