M Das Gupta, DM Gordon, R Hansen, GL Hold, P Pavli, CL O�??Brien
Inflammatory bowel disease (IBD) is a global disease, andit’sprevalence and incidenceisincreasing worldwide along with urbanization.Several lines of evidence implicate bacteria in the pathogenesis of IBD, and Escherichia coli is one of the leading candidates for a pathogenic role. The aim of the present study was to identify genes of E. coli associated with strains isolated from patients with IBD. This study involved whole genome comparisons of 179 E. coli strains, isolated from 64 patients with Crohn’s disease (CD), 18 patients with ulcerative colitis (UC), and 19 controls. Of the 114 isolates from CD patients, 23 were from paediatric patients. Anatomically, 7 were derived from aphthous ulcers, 9 from lymph nodes, and 75 from mucosal biopsies. Of the 33 UC isolates, all were from mucosa. Of the 32 control strains, 29 were from mucosa, 2 from stool, and 1 from bladder. We used A5 MiSeq to assemble the 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.CD-associated E.coli were phylogenetically diverse and did not form a cluster using principal component analysis (PCA). 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 thelymph node strains have properties that allow them to survive intracellularly, within phagolysosomes.