Short-term mucosal disruption enables colibactin-producing E. coli to cause long-term perturbation of colonic homeostasis

ABSTRACT

Colibactin, a bacterial genotoxin produced by E. coli strains harboring the pks genomic island, induces cytopathic effects, such as DNA breaks, cell cycle arrest, and apoptosis. Patients with inflammatory bowel diseases, such as ulcerative colitis, display changes in their microbiota with the expansion of E. coli. Whether and how colibactin affects the integrity of the colonic mucosa and whether pks+ E. coli contributes to the pathogenesis of colitis is not clear. Using a gnotobiotic mouse model, we show that under homeostatic conditions, pks+ E. coli do not directly interact with the epithelium or affect colonic integrity. However, upon short-term chemical disruption of mucosal integrity, pks+ E. coli gain direct access to the epithelium, causing epithelial injury and chronic colitis, while mice colonized with an isogenic ΔclbR mutant incapable of producing colibactin show a rapid recovery. pks+ E. coli colonized mice are unable to reestablish a functional barrier. In turn, pks+ E. coli remains in direct contact with the epithelium, perpetuating the process and triggering chronic mucosal inflammation that morphologically and transcriptionally resembles human ulcerative colitis. This state is characterized by impaired epithelial differentiation and high proliferative activity, which is associated with high levels of stromal R-spondin 3. Genetic overexpression of R-spondin 3 in colon myofibroblasts is sufficient to mimic barrier disruption and expansion of E. coli. Together, our data reveal that pks+ E. coli are pathobionts that promote severe injury and initiate a proinflammatory trajectory upon contact with the colonic epithelium, resulting in a chronic impairment of tissue integrity.

Keywords:

• Inflammtory bowel diseases
• colitis
• microbiota
• mucosal barrier
• colibactin
• E. coli
• stem cells
• regeneration

Author’s contribution

CH and MS designed the study; CH performed most of the experiments and analyses; HB performed bioinformatics analysis of the transcriptome data; H-JM performed and analyzed the microarray; LL performed immunofluorescence staining and analysis; TS provided the mice. The MS was written by CH and MS, and all authors provided feedback.

Acknowledgments

We would like to thank Stefanie Müllerke and Janine Wolff for their excellent technical support, Uwe Klemm, Daniela Groine, Manuela Primke, and the members of the animal facility of the MPI for Infection Biology for their support with the management of the mouse colony, and Rike Zietlow for editing the paper. We also thank the members of the Sigal Lab for their constructive feedback.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

Microarray data have been deposited in the gene expression omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) of the National Center for Biotechnology Information under accession number GSE205403, reviewer token: sxcrkgounnorlmd.

Additional information

Funding

MS received funding from the DFG (Si 1983 3/1 and Si1983 4/1), European Research Council (ERC-Starting Grant REVERT) and the BMBF (PACE Therapy Consortium).