Role of RNA-dependent control in the pathophysiology of Clostridioides difficile and its interaction with the host – CdiffRib

Clostridioides (Clostridium) difficile is the major cause of nosocomial infections associated with antibiotic therapy. The disruption of the colonic microbiota by broad-spectrum antibiotics promotes colonization of the intestinal tract by this pathogen. Due to the increase of severe forms associated with a strong inflammatory response and higher recurrence rates, a current imperative is to develop synergistic and alternative treatments of C. difficile infections. The mechanisms controlling infection cycle of this major human enteropathogen remain largely unexplored. Noncoding RNAs (ncRNA) are in the centre of networks controlling virulence and antibiotic resistance in major pathogens. This project is built upon our genome-scale data on a large diversity of ncRNAs in C. difficile (Transcriptional start site mapping and RNA-seq), the majority being specific to this pathogen, their expression during infection (dual RNA-seq) and interactions with the RNA chaperone protein Hfq (RIP-seq). While the majority of the project will be carried out with the reference strain, we will also extend it to the hypervirulent strain of ribotype 027 having a major clinical impact, to provide insights on the evolution of C. difficile pathogenesis. Our goal is to uncover the biological roles and the molecular mechanisms of RNA-based regulations during C. difficile infections. We will use an integrative interdisciplinary strategy combining genome-wide and targeted molecular biology and genetics, bioinformatics approaches as well as animal models to identify ncRNA targets and regulatory networks and study the impact of riboregulation in C. difficile and during infection in host in particular in the modulation of inflammatory responses. We expect to identify RNA-based mechanisms that contribute directly to the control of C. difficile pathogenicity. These data can be used to develop novel RNA-based diagnostic and therapeutic strategies to limit the development of C. difficile infection.