Canada has one of the world’s highest rates of inflammatory bowel disease (IBD) and newly diagnosed Crohn’s disease (CD) incidence has doubled since 1995. The intestinal bacterial composition of CD patients is altered compared to healthy controls, principally due to the expansion of adherent-invasive Escherichia coli (AIEC). The McPhee lab studies the behaviour of Crohn’s disease-associated E. coli (AIEC) to understand how this group of bacteria induces and adapts to the inflammatory conditions associated with the disease. By utilizing comparative genomic, molecular biological, microbiological, biochemical and immunological techniques, we seek to define the molecular determinants of bacterial fitness under pro-inflammatory conditions.

Projects available include, but are not limited to, the following:

  1. Characterize the mechanism of action of two cationic antimicrobial resistance proteins, ArlA and ArlB. The genes encoding ArlA and ArlB are critical for resistance to cationic antimicrobial peptides, but the biochemical mechanism by which this resistance occurs remains unknown. This project will examine mutant strains of AIEC that are lacking one or both of these proteins to determine what bacterial sites are differentially affected by exposure to cationic peptides.
  2. Express and purify the ArlA and ArlB proteins to enable biochemical characterization. This project aligns with the goals outlined in project 2, whereby we seek to determine the mechanism of action of these proteins in cationic antimicrobial peptide resistance. By constructing affinity-tagged versions of the ArlA and ArlB proteins, these proteins will be purified thereby allowing the development of in vitro assays of protein activity.
  3. Regulation and essentiality of AIEC-enriched metabolic pathways. Unlike other pathovars of coli, the genetic diversity in AIEC is particularly broad. As little is known about which genes/pathways are important for fitness in AIEC, this project will consist of identifying novel genes in clinical AIEC isolates, creating deletions of these genes for phenotypic characterization of the associated mutants as well as creating translational fusions to the promoters of these genes to determine whether and how these genes are regulated.
  4. Mechanisms associated with biofilm formation in IBD-associated E. coli. Histological examination of the mucosal surface of IBD patients has shown that there is a greater propensity for the microbes at the surface to form biofilms. We are interested in determining whether E. coli isolated from patients with IBD have different capacity for biofilm formation as well as what types of genes are required for this activity in different isolates.