Author ORCID Identifier


Date of Graduation


Document Type

Dissertation (PhD)

Program Affiliation

Microbiology and Molecular Genetics

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Anne-Marie Krachler, Ph.D.

Committee Member

Heidi Kaplan, Ph.D.

Committee Member

William Margolin, Ph.D.

Committee Member

Charles Darkoh, Ph.D.

Committee Member

Rosa Uribe, Ph.D.


Inflammatory bowel disease (IBD), including Crohn’s disease and ulcerative colitis, is a broad term for chronic intestinal disorders that severely impact patient morbidity and quality of life. 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 macrophages in vitro. However, how AIEC contributes to IBD in vivo remains unclear. Here a larval zebrafish (Danio rerio) model of AIEC was established, which facilitates the study of the role of pre-existing inflammation, and host- and pathogen- genetic factors during IBD pathogenesis. Paramecium caudatum, a natural prey of zebrafish larvae, was used as a vehicle for AIEC delivery to the gastrointestinal tract, and dextran sulfate sodium (DSS) pharmacologically induced colitis. AIEC colonized the zebrafish gut in higher numbers and persisted for longer compared to non- pathogenic E. coli in the absence of chronic inflammation. Further, bacterial burden and persistence in the host were higher in fish with pre-existing DSS colitis. The proinflammatory response was further exacerbated by AIEC, resulting in higher neutrophil recruitment to the gut and increased relative expression of the genes that encode proinflammatory cytokines. In addition, we showed that two AIEC virulence factors, FimH and IbeA, play a role in AIEC colonization and contribute to intestinal inflammation in larval zebrafish, similarly to what has been observed in mice. In conclusion, we established a high-throughput, genetically tractable model to study AIEC–host interactions in the context of chronic inflammation.


larval zebrafish, inflammatory bowel disease, adherent-invasive E. coli