M Das Gupta, DM Gordon, R Hansen, GL Hold, P Pavli and CL O'Brien
Several lines of evidence implicate bacteria in the pathogenesis of inflammatory bowel disease (IBD), and Escherichia coli is one of the leading candidate triggers. Our aim was to identify genes of E. coli associated with IBD.This study involved whole genome comparisons of 179 E. coli strains, isolated from 64 Crohn’s disease (CD) patients, 18 ulcerative colitis (UC) patients, and 19 controls. These isolates were obtained from different tissues and sources, such as aphthous ulcers, lymph nodes and intestinal mucosa. We used A5 MiSeq to assemble sequences, PROKKA for annotation, ROARY for pan-genome analyses, and SCOARY to assess phenotype-genotype relationships. We determined the serotype, sequence type (ST), virulence genes, plasmids, bacteriophage, CRISPRs, capsules, bacteriocins, and antibiotic resistance genes for each strain. CD-associated E. coli were phylogenetically diverse. The most abundant E. coli phylogroup was B2 and the most common ST was ST95. The E. coli UTI89 plasmid was significantly associated with paediatric CD isolates compared with controls. Based on total gene content, CD isolates were significantly associated with particular genes associated with adhesion, the toxin-antitoxin system, plasmid partitioning, conjugation transfer, and signal recognition when compared to controls. Genes associated with adhesion and invasion and peroxide scavenging were significantly associated with lymph node E. coli isolates from CD patients. Our findings suggest that CD-associated E. coli are associated with genes involved in adhesion, and the lymph node strains have properties that allow them to survive intracellularly, within phagolysosomes. This study provides insights into the potential role of E. coli in the pathogenesis of IBD
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