Public Health Agency of Canada
Impact of antimicrobial use on antimicrobial resistance (AMR) in foods using risk science and genomics data
The Public Health Agency of Canada is participating in year 4 of a 5-year interdepartmental collaborative research project to use a genomics-based research approach to investigate how food production contributes to the development of AMR of human health concern, and explore strategies for reducing AMR in food production systems.
New genomic information could have a profound impact on the assessment of how antimicrobial use in livestock impacts AMR in foods. Historically, activities such as risk profiling, risk assessment, and mathematical modelling for foodborne AMR have used phenotypic information to consider risks from AMR in foods. Methods for incorporating genomic information into these activities are only now being established. The rapid uptake of whole genome sequencing (WGS) and other genomic tools, in part attributed to their declining cost, suggests that public health officials can expect a wealth of new information on the occurrence and transmission of AMR through the food chain. It is crucial to identify best practices for incorporating such information into foodborne AMR risk science to address questions from decision makers to reduce impacts of AMR on public health.
The Agency is currently developing a suite of tools to estimate the relative impacts of food production and processing practices on AMR in foods. Such tools include an integrated assessment model to consider the impacts of protective or risk factors on exposure to different AMR profiles in various food commodities, risk profiles to qualitatively describe select AMR food safety issues, a threat assessment to rank various AMR food safety issues, and a quantitative microbial risk assessment to explore impacts of farm-to-fork interventions on a specific AMR food safety issue. WGS data are being produced by partners throughout the project. The candidate will develop and apply novel methods for interpreting genomics data collected along the agri-food chain in the current suite of tools, alongside a network of experts in bioinformatics, epidemiology, modelling, and risk assessment. Following this, the candidate will be primarily responsible for comparing the utility of each tool in the context of 1) integration of genomic data and 2) providing insights into how AMR impacts human health through the agri-food chain.
Duration: Now through March 2021, with potential for continued funding.
Education: PhD or equivalent in Bioinformatics, Epidemiology, Engineering, Mathematics, Statistics, or similar
- Experience in epidemiology, risk science and/or statistical analyses
- Experience leading projects and coordinating research
- Knowledge of risk analysis principles
- Knowledge of AMR in the food chain
- Knowledge of bioinformatics and/or genomics
- Knowledge of foodborne diseases and microbiology
- Time management and organizational skills
- Strong written and oral communication skills
- Ability to conduct statistical analyses
- Proficient with computer programs (e.g., @Risk, Analytica, Microsoft Office)
- Effective interpersonal skills
- Able to work independently and as part of a team
- Reliable, with strong initiative
Government Classification and Salary Range
SE-RES Scientific Research
Scientific Researchers (SE-RES) salary levels are incumbent-base. Therefore, the level of the position will be determined by the qualifications/ accomplishments of the successful candidate. As the PRP is for researchers at the beginning of their careers, starting salaries usually range between $55,870 and $86,853.
Candidates must have obtained a doctoral degree (PhD) within the last three (3) years from a recognized post-secondary institution in a field of natural sciences with a specialization related to the duties of the position.
Please email a CV, cover letter that describes how you meet the requirements, and three referees, as a single PDF file, to Ben Smith (PHAC) at Ben.Smith@Canada.ca
 Special consideration may be given to applicants who were unable to apply during the 3-year period, due to a significant career interruption or delay.