Post-doctoral researchers in bioinformatics – AMR surveillance

Antimicrobial resistance (AMR) is one of the largest human health concerns of this generation, as the continued emergence of resistance threatens to interfere with our ability to treat and prevent human infectious diseases.

Combating AMR requires a One Health approach, combining efforts at limiting resistance emergence and spread within human, animal and environmental reservoirs. As all use (including responsible use) contributes to potential resistance, and transfer can occur between sectors, developing a standardized surveillance platform is imperative. We are currently seeking two computational hires to work collaboratively on two separate, yet integrated, research programs. The first project builds on the recently developed amplicon-based platform termed Diversity of Antibiotic Resistance genes and Transfer Elements – Quantitative Monitoring, abbreviated as DARTE-QM (Smith et al. 2022 Communications Biology, 5 (1): 1-9). This initial version of the platform targeted 662 antibiotic resistance genes and was employed across a diversity of complex environmental samples including manure, soil and livestock feces and illustrated the potential of this platform to both distinguish the resistomes of each source and to allow for comparisons of resistance diversity and abundance across sectors. We are now initiating the second phase of development, aimed at prioritizing our primer targets based on risk characterization and prevalence, and further optimization of the platform. This work will be performed in collaboration with the Canadian Integrated Program for Antimicrobial Resistance (CIPARS) and the Comprehensive Antimicrobial Resistance Database (CARD) and a diversity of researchers from Iowa State University, University of Guelph, and McMaster University. The second project will develop schema and computational pipelines for the incorporation of antimicrobial resistance data into the AgriFood Canada Database for use across a diverse collection of collaborators, including the National Microbiology Laboratory, Public Health Agency of Canada and Animal Health Laboratories.

Funding for these projects, including competitive post-doctoral salaries, has already been secured and a start date of January 1, 2023 is preferred but is negotiable.

General Outline of Duties: Development of computational analysis pipelines for metagenomic and amplicon-based bacterial community data, database management, literature review and critical analysis, experimental design, primer development, data management and analysis, maintenance of data deposition records and documentation, manuscript preparation, supervision and training of graduate students

Teaching Requirement: There are no formal teaching requirements but teaching experience can be arranged

Student/Employee Supervision: Supervision of bioinformatics and graduate students will be expected

Required Qualifications: The successful candidate will have a relevant PhD in bioinformatics, computational science, or biological science with significant relevant experience. Experience in metagenomics, bacterial genetics and/or antimicrobial resistance is a significant asset as well as strong programming skills (e.g. Python, R, Perl, etc.) and good knowledge of relational database (e.g. MySQL).