Gnotobiotic OMM12 mice support sustained Clostridioides difficile colonization without antibiotic pretreatment

Abstract

Antibiotic-induced disruption of the intestinal microbiota predispose individuals to Clostridioides difficile infection (CDI). Although several animal models reproduce acute CDI, sustained colonization in the presence of a defined resident microbiota remains challenging to study. Here, we show that gnotobiotic OMM12 mice support sustained colonization for at least 20 days following oral challenge with either the reference CD630{Delta}erm strain or the clinical R20291 (RT027) strain, without prior antibiotic treatment. Early infection induced transient weight loss, rapid intestinal inflammation and transient shifts in the relative abundance of resident bacterial species. By day 20, inflammatory markers had largely resolved, and the resident microbiota had shifted back towards its baseline composition, despite continued detection of C. difficile vegetative cells, spores and toxins. Early bacterial community perturbations were not accompanied by detectable changes in the resident prophage induction. Moreover, whole-genome sequencing of C. difficile clones recovered at day 20 showed no detectable gut-specific genomic adaptation relative to the inoculum. Similar colonization kinetics and clinical outcomes were observed across independent experiments conducted over five years, supporting the consistent reproducibility of this model. Together, OMM12 mice provide a defined, antibiotic-free and experimentally tractable framework to investigate host-microbiota-pathogen interactions during sustained C. difficile colonization and a robust platform for therapeutic development.