Composition and Pathogenic Potential of Mucosal Microbiota in Ulcerative Colitis

Objective: There is a large amount of data on fecal microbiome composition in inflammatory bowel disease and ulcerative colitis, but the mucosal microbiome is less described. Analysis of pathogenic determinants of microorganisms colonizing inflamed regions is promising for understanding their role in disease pathogenesis. The aim of this study is to compare the microbiome composition of ulcerated and non-inflamed areas and to evaluate the pathogenic potential of Escherichia coli isolates from damaged epithelial samples of ulcerative colitis patients. Methods: In this study, we investigated the mucosal microbiota of ulcers and non-inflamed areas of 25 patients with UC from the Southern European part of Russia. We described a composition of mucosal microbiome using 16S rRNA sequence analysis and characterized E. coli isolates from ulcers for antibiotic susceptibility, presence of virulence factor genes, and phylogenetic group distribution. Results and Discussion: Most of the E. coli isolates from ulcers were multidrug resistant, including 7 isolates with resistance to more than 7 antibiotics, and carried virulence factor genes (hly, 23%; pap, 38%; cnf, 42%). The combination of these markers and the determined phylogroup profile indicates a pathogenic potential of E. coli localized in patients’ ulcers and a possibility of development of intestinal and extraintestinal infections. Metagenomic analysis revealed a high similarity of microbial populations in non-inflamed areas and ulcers of different localization. Conclusions: The composition of the intestinal mucosal microbiota in ulcerative colitis is characterized by a low degree of variation between ulcerated and non-inflamed areas. At the same time, a pathogenic potential of E. coli isolates is observed. Our results support the importance of personalized antibiotic therapy prescription and patient monitoring to prevent opportunistic infections in the treatment of UC.