Colonization of larval zebrafish (Danio rerio) with adherent-invasive Escherichia coli prevents recovery of the intestinal mucosa from drug-induced colitis

Inflammatory bowel disease (IBD) is a broad term for a range of chronic intestinal disorders, including Crohns disease and ulcerative colitis. The global prevalence of IBD is rising, with over one million patients affected in the US alone. Adherent-invasive E. coli (AIEC) is a pathobiont frequently found in IBD biopsies. AIEC adhere to and invade epithelial cells, and can survive inside phagocytes in vitro. However, how AIEC contribute to IBD in vivo remains unclear. Here, we established a larval zevbrafish (Danio rerio) model to study the interplay between pre-existing intestinal inflammation and AIEC colonization of the gut. We used the pro-inflammatory drug dextran sulfate sodium (DSS) to induce colitis. This was followed by food-borne infection of larvae with AIEC using the protozoan Paramecium caudatum, a natural prey, as a vehicle. We show that AIEC more robustly colonizes the zebrafish gut, and persists for longer, compared to non-pathogenic E. coli. In addition, DSS induced colitis increases both bacterial burden and persistence in the larval gut. We benchmark our model against existing rodent models using two mutants deficient in the known AIEC virulence factors FimH and IbeA, which have virulence defects in both rodent and the larval zebrafish model. Finally, we show that AIEC colonization exacerbates DSS induced colitis and prevents recovery from inflammation. In conclusion, we established a high-throughput, genetically tractable model to study AIEC-host interactions in the context of chronic inflammation. IMPORTANCEAlthough inflammatory bowel diseases are on the rise, a lot remains to be learned about the link between IBD severity and the underlying cause. Although host genetics, microbiome, and environmental factors have all been shown to correlate with the development of IBD, cause and effect are difficult to disentangle in this context. For example, AIEC is a known pathobiont found in IBD patients, but it remains unclear if gut inflammation during IBD facilitates colonization with AIEC, or if AIEC colonization makes the host more susceptible towards pro-inflammatory stimuli. To develop successful therapeutics, it is critical to understand the mechanisms that contribute to AIEC infections in a susceptible host. Here, we show that the larval zebrafish model recapitulates key features of AIEC infections in other animal models, and can be utilized to address these gaps in knowledge.