Microbiota mechanisms promoting Clostridioides difficile colon persistence

Project Summary Clostridiodes difficile is an opportunistic enteric pathogen which can cause critical and even fatal colonic disease. Of the nearly 500,000 reported Clostridioides difficile infection (CDI) cases annually, a particularly unique challenge facing clinicians is the striking level of recurrence of C. difficile disease (rCDI) following treatment, which can range anywhere from 20-45%. Though it has been well described in the literature how host microbes promote colonization resistance to prevent primary C. difficile infection, the molecular mechanisms of the colon microbiota that govern the persistence, or clearance, of C. difficile’s are still under investigation. We propose that one of the factors that governs the persistence of C. difficile within the host is the associated colon bacterial community. Consistent with this hypothesis, studies that investigate the community composition of rCDI patients highlight particular microbial signatures in this population compared to non-infected or non-recurrent controls, specifically, an increased abundance of Proteobacteria. The preliminary data outlined in this proposal demonstrate that certain Proteobacteria, such as Klebsiella pneumoniae (Kp) and Escherichia coli (Ec), create an environment that modulates the metabolomic profile of C. difficile. Our results suggest that Kp and Ec, through mechanisms we plan to explore through this research, induce C. difficile to produce indole-3-acetic acid (IAA), which can directly promote an anti-inflammatory phenotype in the host mucosa through engagement of the aryl hydrocarbon receptor (AhR). We hypothesize that in some microbial contexts, such as those prompted by CDI standard of care antibiotic treatment in which Proteobacteria bloom, C. difficile can shift to produce IAA which in both AhR-dependent and -independent mechanisms creates an immunotolerant environment. Furthermore, our preliminary data demonstrate that not only may IAA act on the host but appears to have important impacts on the virulence of the pathogen through the upregulation of C. difficile sporulation and production of its primary C. difficile toxin, TcdB. We suggest that both tolerance at the host mucosa as well as changes in pathogen virulence allows C. difficile to persist at the host mucosa, creating conditions ripe for the development of rCDI. Through the completion of this project, we plan to define both the host and microbial contributions to this mucosal immunotolerance pathway potentially conducive to C. difficile persistence, with the long-term goal of identifying putative biomarkers in the stool of patients who are increased risk of recurrent infection.