Unravelling the role of microbiome and Escherichia coli as a trigger for Inflammatory Bowel Disease with a particular focus on Crohn's disease.

Abstract

Inflammatory bowel diseases (IBD) are chronic inflammatory conditions of the digestive tract consisting of two primary forms: Crohn's disease (CD) and ulcerative colitis (UC). The pathogenesis of IBD is still not precisely known. However, an imbalance in the intestinal microbiome (dysbiosis) and putative pathogens have been implicated. Several lines of evidence implicate bacteria in the pathogenesis of IBD, and Escherichia coli (E. coli) is one of the leading candidate triggers. These studies aimed to investigate the role of gut bacteria with a particular focus on E. coli, to determine if genes or molecular properties of E. coli are associated with tissue type, including lymph nodes and the initial CD lesion (aphthous ulcer), or adult and paediatric isolates. We also aimed to determine the association of genes and molecular properties of E. coli with NLRP3 inflammasome activation, which may be a mechanism that causes CD. The microbiome analysis was based on 16 non-BD controls and 72 CD tissue samples. CD tissue samples consisted of tissues from active and inactive stages of disease; 'early-active-stage' tissues, including aphthous ulcers; 'mid-stage tissues', which included biopsies obtained during colonoscopy; and 'late-stage' tissues, obtained from surgical resections. We found that CD at different disease stages was associated with a microbial signature characterised by reduced alpha diversity and greater dysbiosis compared to controls. Several genera were significantly increased in CD and different disease stages compared to control, including Escherichia_Shigella, Flavonifractor, Klebsiella, and Ralstonia. In contrast, Faecalibacterium was markedly reduced in CD and different disease stages compared to controls. E. coli have been implicated in CD, but the molecular properties or genes that may contribute to their potential virulence are undetermined. The comparative genomics analysis involved the whole-genome comparisons of 179 E. coli strains, isolated from 62 patients with CD (n = 23 paediatric CD), 18 with UC, and 20 controls. The source of the isolates included lymph nodes (n = 13), aphthous ulcers (n = 7), intestinal mucosa (n = 133), and other sources (n = 26). Bottromycin bacteriocin, ABC capsule, and E. coli pUTI89 plasmid were significantly associated with paediatric CD. In contrast, Group IV e capsule and Bottromycin bacteriocin were significantly associated with lymph node CD isolates compared to controls. CD isolates were more likely to have genes associated with adhesion, the toxin-antitoxin system, plasmid partitioning, and conjugation than healthy controls. Lymph node CD isolates were associated with genes involved in adhesion, phosphate binding and catalase-peroxidase activity than controls. Catalase-peroxidase activity may allow E. coli to survive within lymph nodes, consequently providing an ongoing stimulus to the immune system. Mechanisms that allow E. coli to remain viable in lymph nodes of patients with CD should be explored by in vitro studies and with a larger sample size. It has been hypothesised that damage to the intestinal mucosa occurs in patients with CD due to a dysregulated innate immune response triggered by microbial antigens in genetically susceptible individuals. Previous studies showed that the NLRP3 inflammasome was associated with the secretion and release of mature IL-1beta and IL-18, enhancing intestinal inflammation. We explored whether E. coli activate the NLRP3 inflammasome in mouse bone marrow-derived macrophages, focusing on different molecular properties and genes and their ability to activate the NLRP3 inflammasome. Although activation of NLRP3 was not associated with the clearance of E. coli from macrophages, we found the association of some genes of E. coli strains with inflammasome activation. Several features, such as small toxic polypeptides that are beneficial for E. coli to survive inside the macrophages, may be a mechanism that causes CD. Show more