The role of bacterial, fungal, and viral infections in the pathogenesis of inflammatory bowel disease
Authors:   I.I.Mechnikov North-Western State Medical University, Saint Petersburg, Russian Federation, Sitkin S.I. ,   Almazov National Medical Research Centre, Saint Petersburg, Russian Federation,   Institute of Experimental Medicine, Saint Petersburg, Russian Federation, Avalueva E.B. ,   I.I.Mechnikov North-Western State Medical University, Saint Petersburg, Russian Federation, Bakulin I.G. ,   I.I.Mechnikov North-Western State Medical University, Saint Petersburg, Russian Federation, Skalinskaya M.I. ,   I.I.Mechnikov North-Western State Medical University, Saint Petersburg, Russian Federation, Vorobyev S.L. ,   National Center for Clinical Morphological Diagnostics, Saint Petersburg, Russian Federation, Pavlova E.Yu. ,   I.I.Mechnikov North-Western State Medical University, Saint Petersburg, Russian Federation, Khavkin A.I. ,   Scientific Research Clinical Institute of Childhood Ministry of Health of the Moscow region, Moscow, Russian Federation,   Belgorod National Research University, Belgorod, Russian Federation
Published: August 2023

Inflammatory bowel disease (IBD) is a group of phenotypically similar diseases characterized by multiple organ damage with predominant localization in the gastrointestinal tract and conditionally divided into two nosologies, ulcerative colitis (UC) and Crohn's disease (CD). IBD is closely associated with taxonomic and functional dysbiosis, however, to date, no study has confirmed that a single specific microorganism is the direct cause of IBD according to Koch’s postulates. The complexity of the etiology and pathogenesis of IBD determines the high interest in studying the infectious factor, not as the only causally significant factor, but as a trigger and/or comorbid one. The review summarizes current data on the involvement of the most important microorganisms (pathogens, opportunistic microorganisms, and pathobionts) in the pathogenesis of UC and CD and considers their possible role in the induction, progression, and course of IBD. A possible relationship between IBD and bacteria belonging to the phyla Pseudomonadota ( Proteobacteria), Bacillota ( Firmicutes), Actinomycetota ( Actinobacteria), and Spirochaetota, archaea, fungi, and eukaryotic viruses is discussed. Bacteria such as adhesive-invasive strains of Escherichia coli (AIEC), Salmonella enterica Typhimurium, Campylobacter jejuni, Campylobacter concisus, enterohepatic species of Helicobacter (including Helicobacter bilis), Proteus spp., Aeromonas spp., Klebsiella pneumoniae, Yersinia enterocolitica, Clostridioides difficile, Enterococcus spp., Staphylococcus aureus, Mycobacterium avium subsp. paratuberculosis and Brachyspira spp. The involvement of methanogenic archaea, such as Methanobrevibacter smithii and Methanosphaera stadtmanae, in immunoinflammatory processes in IBD has been shown. The pro-inflammatory role of intestinal fungi Candida albicans, which produces the cytolytic toxin candidalysin, Candida tropicalis, which forms polymicrobial biofilms, and Debaryomyces hansenii, has been revealed. The role of eukaryotic viruses such as herpesviruses (cytomegalovirus, Epstein–Barr virus, human herpesvirus 6), enteropathogenic viruses (norovirus), enterovirus B, hepatitis B virus (Orthohepadnavirus) in the development of IBD is discussed. Particular attention is paid to the possible role of the SARS-CoV-2 (COVID-19) virus as a trigger of IBD. Key words: inflammatory bowel disease, infections, archaea, bacteria, viruses, fungi, dysbiosis, gut microbiota