Project Snapshot

Surveillance Pillar

Molecular Epidemiology of Antimicrobial Resistance in Enterococcus From Poultry, Cattle, Humans, and the Environment

Project Key Words: Enterococci, Comparative Genomics, Virulence, Antimicrobial Resistance

Principal Investigator: Sylvia Checkley, PhD; Tim McAllister, PhD

Co-Investigator(s): Karen Liljebjelke, PhD; Rahat Zaheer, PhD; Susan Cork, PhD, Richard Reid-Smith PhD, Simon Otto PhD, Cheryl Waldner PhD, Sheryl Gow PhD

Trainees: Lindsay Rogers, DVM; Kayla Strong, MA; Alyssa Butters, DVM

Project Theme: Innovation and Commercialization

The Aim

Using whole genome sequencing (WGS) data, this project aims to assess the genetic relatedness of core genomes, mobile genetic elements and  antimicrobial resistance genes (ARG) of Enterococcus sourced from poultry farms, beef feedlots, and retail meat products. In collaboration with WP3a and WP3b, we will  predict the AMR phenotype using bioinformatics approaches, and use an integrated assessment model to determine potential transmission of resistant bacteria and associated public health risks.

Why is this important?

Enterococci are leading causes of nosocomial infections.  Specifically, E. faecium and E. faecalis represent opportunistic nosocomial pathogens that cause difficult-to-treat infections as a result of intrinsic and acquired antimicrobial resistance.  Entercocci are also prevelant in livestock and poultry where they often exhibit high levels of resistance to macrolides, a family of antibiotics considered of high importance in human medicine. Entercocci can also be used as an indicator of fecal contamination.


  • Inform surveillance and policy through
    • Better understanding of the relatedness of enterococci isolated from different sources,
    • Modelling enterococci and ARG transmission dynamics,
    • Comparison of resistant phenotypes and genotypes.
  • Information that supports the mitigation of AMR.

Research Questions

  1. What is the distribution of specific MGE and AMR genes in E. faecium and E. faecalis across different sources?
  2. What is the correlation between AMR genotype and phenotype in enterococci?
  3. Can we use modelling techniques to better understand the transmission of ARG and associated risk?

Our Approach

We use a One Health approach to investigate this issue. We will complete a scoping review as well as use comparative genomics, molecular epidemiology, and sophisticated bioinformatics tools with an extensive “One Health” collection of enterococci from humans, livestock, poultry, sewage, surface water, lagoons, and meat processing plants. In addition, use of an integrated assessment model and other epidemiologic techniques will be used to look at specific associations between outcomes and risk factors.

Research questions 2 and 3 have linkages with Project 3a (AMR phenotype prediction tool development component) and 3b (integrated assessment modeling component), respectively.

Leveraged Sources of Support

  • Genome Canada
  • Beef Cattle Research Council
  • UofA, UofC and AAFC - Infrastructure

Knowledge & Technology: Exchange and Exploitation

  • Identification of new tools for the management AMR throughout the One Health environment.
  • Validate tools and develop operating procedures for adoption by industry.

Highly Qualified Personnel

  • 3 MSc Students