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. Regulation and function of outer membrane proteases in enteric bacteria. Bacteria have evolved complex regulatory systems to combat the host antimicrobial activity. Among these responses are outer membrane embedded proteases that can degrade host defense peptides. We seek to understand both how these are regulated and how different proteins contribute to bacterial behaviour.
  2. 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.
  3. Effects of AIEC infection on macrophage behaviour. Macrophages from IBD patients exhibit altered behaviour, including decreased killing ability and altered cytokine responses. We are interested in understanding how IBD-associated E. coli contribute to these altered behaviours.
  4. 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.
  5. 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.
  6. Heterogeneity in bacterial signaling systems. Bacteria have conserved two-component regulatory systems and these systems play a crucial role in how bacteria respond to different environments, including virulence. Different strains of the same bacteria can have very different behaviour in response to identical conditions. We seek to characterize these differences as well as understand the effects it has on bacterial behaviour.