The role of gastrointestinal pathogens in inflammatory bowel disease: a systematic review

The inflammatory bowel diseases (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC), are chronic, progressive, inflammatory conditions of the gastrointestinal tract. Imbalance in the gut microbial community, or dysbiosis, and the subsequent immune response, represent the critical relationship between genetic susceptibility, microbes, and environment factors, that result in IBD. Gastrointestinal pathogens - a common cause of dysbiosis - have been implicated as an environmental trigger in new onset IBD, as well as flare of existing IBD. In this article, we systematically review clinical data regarding the association between specific gastrointestinal pathogens and IBD. Numerous bacteria, viruses, fungi, and parasites have been implicated in the pathogenesis of IBD, and exacerbations of existing disease. In this article, we will also specifically discuss the less recognized microbes that have an inverse association with IBD, including certain bacterial pathogens, such as Helicobacter pylori, and parasites, such as Trichuris species. Future prospective and experimental studies are required to establish causality and clarify potential mechanisms of enteric pathogens in modifying the risk and course of IBD.

Systematic review: gastrointestinal infection and incident inflammatory bowel disease

BACKGROUND

The initiating events of chronic gastrointestinal (GI) inflammation in Crohn's disease (CD) and ulcerative colitis (UC) are not well-defined, but GI infections are implicated.

AIMS

To define the role of GI infections in risk of incident inflammatory bowel disease (IBD) and synthesise the current body of relevant translational data to provide biological context for associations between GI infections and IBD risk.

METHODS

We systematically reviewed electronic databases through February 2020. Clinical studies that provided risk estimates of the association between GI infections and incident IBD were included. Inclusion criteria were broader for translational studies aiming to define mechanisms of GI infections and predisposition to or protection from IBD.

RESULTS

Of the studies identified, 63 met full inclusion criteria. Among studies of clinical gastroenteritis, bacteria-specifically, Salmonella species, Campylobacter species and Clostridioides difficile-demonstrated consistent positive associations with risk of incident IBD. Of viruses, norovirus was associated with increased risk of incident CD. Regarding inverse associations with incident IBD, Helicobacter pylori and helminth infections were associated with a generally consistent reduced risk of IBD. Based on a qualitative analysis of the translational data, putative mechanisms involve multiple microbial and immunologic pathways.

CONCLUSIONS

Based on this systematic review, certain enteric pathogens are associated with an increased risk of incident IBD, while others are potentially protective. Prospective studies are required to clarify the clinical implications of these enteric pathogens on the risk and course of IBD, and possible therapeutic or preventative benefit.

Integration of multi-omics data from re-wilded laboratory mice to identify key parameters that determine immune heterogeneity and activation

Current research on immunology are largely based on clean laboratory mice kept in specific pathogen free (SPF) environments. They have the advantage of being inbred, genetically homogeneous and can be manipulated genetically in disease models. However, humans as with all free-living mammals face a more complex environment and are exposed to various food resources, microbial experiences, thermogenic changes, and must constantly respond to environmental challenges. We have established a unique experimental system in which laboratory mice are “re-wilded” through release into an outdoor enclosure facility. Here, we use multi-parameter assays including 16S/Metagenomic sequencing, intestinal RNA-sequencing, and 34 parameters of flow cytometry to explain heterogeneity of immune responses from exposure to the wild environment. Increased immune activation of re-wilded mice occur in the absence of viral, bacterial or parasitic pathogen exposure in this enclosure, including increase of CD4+ and CD8+ memory T cells, effector T cells, innate lymphoid cells (ILCs), circulating neutrophils, reduction in naïve T cells, and increased expression of costimulatory molecules on antigen presenting cells. When we examined cytokine production in response to ex vivo stimulation of mesenteric lymph node cells with 8 bacterial and fungal stimuli, the mesenteric lymph node cells from re-wilded mice are poised for different responses via robust induction of cytokines than laboratory mice. By using machine learning models, we are integrating these multi-omic datasets to better predict the association between environmental and host genetic factors on driving heterogeneity of immune responses in the re-wilded mice.