Bioinformatics of Clinical and Environmental Fungi and Bacteria

The Cumming School of Medicine and Faculty of Science at the University of Calgary are accepting applications for a Postdoctoral Scholar in Bioinformatics and its application to Wastewater-Based Surveillance (WBS) of antimicrobial resistance and emerging pathogens.

The postdoc will be part of an interdisciplinary research team that uses wastewater to track the dynamics of infectious agents. We have developed an integrated surveillance network monitoring 43 municipalities, as well as several sentinel surveillance hubs including a large number of tertiary care hospitals and populations of special interest from which we collect samples 1-3x per week.  Wastewater data can be compared with population-level data and hospital-specific data drawing from a single provincial health provider – and the potential of this unique network is exceptional. To date we have amassed >2000 samples that have been processed as raw wastewater and culture enriched raw wastewater (for specific pathogens).  A parallel agriculture and agri-food network is being developed which will be further leveraged.  The postdoc will work directly with a transdisciplinary team of clinicians and researchers at the University of Calgary (Cumming School of Medicine and Faculties of Science, Engineering, and Veterinary Medicine, and Advancing Canadian Water Assets (ACWA)) and their collaborators including those at the Universities of Alberta, Athabasca and Lethbridge. The Postdoc will also have the opportunity to collaborate with public health, pharmacy, infection control, and antimicrobial stewardship experts at Alberta Health Services.

The successful applicant will join a productive transdisciplinary team with supporting research funding from NSERC, CIHR, Genome Alberta, and Alberta Health. Working with the Primary Investigators Michael Parkins and John Conly (Cumming School of Medicine, Departments of Medicine and Microbiology, Immunology & Infectious Diseases) and Casey Hubert (UCalgary Research Chair, Faculty of Science). The Postdoc will work as part of a large team that includes several HQP staff and trainees including those in graduate, undergraduate and post graduate training programs.  There will be abundant opportunities for collaboration with others interested in bioinformatics and mentorship of junior trainees.

The successful candidate will be based at the University of Calgary and utilize archived (>2000 samples to date) and newly collected wastewater samples for bioinformatics and molecular analyses for the detection of bacteria, fungal and viral pathogens and antimicrobial resistance genes. The candidate will be exposed to multiple teams with complementary skillsets working across a range of labs and campuses. This position will utilize our existing research capacity in field sampling to follow with molecular detection using nucleic acid sequencing (amplicon and/or shotgun) based approaches. Applying or developing bioinformatics analysis pipelines is an essential part of this work. This postdoc will play a key role in our team’s efforts to disseminate information, and there will be abundant opportunities to contribute to peer-reviewed publications and presentations. Accordingly, contributing to the preparation of manuscripts will be a high-priority objective for this position. Additional responsibilities will include participating in and supporting the team described above and some supervision of junior colleagues.

• PhD in bioinformatics, molecular biology, microbiology, or a related field.
• Strong experience in (meta)genomics or bioinformatics, preferably antimicrobial resistance or wastewater environment
• Experience in scripting in Python and/or R, use of software for genomic or metagenomic analysis, and data visualization
• Experience with biostatistical approaches is desirable
• Understanding of analytical methods, particularly in molecular microbiology
• Must be able to work in a team environment and interact with a diverse range of colleagues and collaborators.
• Strong communication skills as well as good organizational, time management, and problem-solving skills
• Ability to work independently and resourcefully, while interacting effectively with internal and external stakeholders at all levels of the organization
• Able to work within a collaborative setting with others to set clear priorities while managing multiple timelines and objectives
• Evidence of good research productivity
• Strong academic writing potential