Colonic epithelial regeneration shapes susceptibility to Clostridioides difficile infection

Clostridioides difficile infection (CDI) susceptibility and severity are strongly associated with preexisting colonic inflammation. However, chronic inflammatory conditions such as cystic fibrosis rarely progress to symptomatic CDI despite high rates of C. difficile colonization, suggesting that inflammation alone is insufficient to explain disease vulnerability. Notably, populations relatively protected from symptomatic CDI exhibit impaired regenerative capacity within the colon epithelium. Here, we used single cell RNA sequencing of human colonoid monolayers to map markers of CDI susceptibility and severity to cell populations associated with inflammation and epithelial repair. We identified an inducible microfold-like (M-like) population that is largely absent from the healthy colon but emerges during inflammation and regeneration. These cells were enriched for markers of severe CDI, C. difficile toxin interaction genes, and elevated CCL20 and CFTR expression. Spatial imaging localized CCL20-producing cells to wound-like gaps in mock and CDI-treated colonoids, identifying a repair-associated niche active independent of infection. Following exposure to C. difficile, wound-healing transcription within the M-like lineage declined while tuft-like populations expanded and upregulated genes associated with immune cell recruitment. These findings demonstrate that epithelial regeneration shapes host CDI vulnerability.