Toronto infectious disease community tackles antimicrobial resistance from multiple angles
A smiling woman with a grey sweater and a smiling man wearing a toque and blue coat

(Photo by Roberto Sorin on Unsplash)

November 23, 2023

By Betty Zou

Earlier this year, the federal government released its Pan-Canadian Action Plan on Antimicrobial Resistance, which details federal, provincial and territorial commitments to address antimicrobial resistance (AMR) across the five pillars of research and innovation, surveillance, stewardship, infection prevention and control, and leadership.

To mark World AMR Awareness Week, we are celebrating some of the contributions from the EPIC community to accelerate progress towards achieving the goals set out within the action plan.

What is AMR and why should you care?

Effective drugs to treat bacterial, viral, fungal and parasitic infections are the unsung heroes of modern medicine but their ability to save lives is being curtailed by the growing spread of AMR.

Resistance arises when microbes naturally evolve to become resistant to drugs meant to kill them. Without antimicrobials, common infections can become life-threatening and routine procedures like surgery, chemotherapy and C-sections could become significantly more risky. Drug-resistant infections also have impacts on the economy and health care systems, resulting in longer hospital stays and lost productivity.

The World Health Organization has declared AMR one of the top 10 global health threats facing humanity. According to a 2022 study published in The Lancet, there were an estimated 4.95 million deaths associated with AMR in 2019. Of those, 1.27 million were directly attributable to infections caused by drug-resistant bacteria.

Here in Canada, a 2019 report estimated that drug-resistant bacterial infections were associated with the deaths of over 14,000 people in this country in 2018. That same year, AMR was estimated to have cost the health care system $1.4 billion and reduced GDP by $2.0 billion.

Research and innovation

A collaborative new project co-led by EPIC members Nicole Weckman and Rob Kozak is helping to achieve one of the desired outcomes laid out in the action plan’s research and innovation pillar — expanded scientific knowledge base and tools to guide effective antimicrobial use and AMR-related interventions.

The project brings together Weckman’s engineering expertise with Kozak’s clinical microbiology experience to create a rapid diagnostic tool that can accurately detect the drug resistant fungal pathogen Candida auris. The test repurposes gene editing CRISPR technology to identify fungal DNA and detect genetic mutations known to confer resistance to different classes of antifungal drugs.

Supported by an EPIC New Connections Grant, the team will develop the diagnostic assay at U of T, where Weckman is the Paul Cadario Chair in Global Engineering, and validate it at the Shared Hospital Laboratory based at Sunnybrook Health Sciences Centre, where Kozak is a clinical microbiologist.

“Drug resistant fungal infections pose a significant threat to public health, particularly for vulnerable populations like the elderly and immunocompromised,” says Weckman. “This tool addresses an urgent need for diagnostic tests that can provide fast and accurate results to clinicians and frontline staff so that they can make the most informed decisions about patient care and infection control.”


Despite the WHO’s classification of C. auris as a fungal pathogen of critical priority, only British Columbia and Alberta require mandatory reporting of C. auris infections. To address this critical gap in surveillance, Public Health Ontario (PHO), along with other provincial laboratories, is taking part in a voluntary national effort to track C. auris cases in Canada. In Ontario, the initiative involves clinical labs sending samples to PHO and the National Microbiology Lab in Winnipeg for confirmation and characterization.

“Currently, case counts remain low in Canada so now is the time to ensure labs have appropriate screening programs in place to prevent spread of this very challenging drug resistant pathogen,” says Julianne Kus, a clinical microbiologist at PHO.

Kus notes that currently not all labs and healthcare facilities are screening for C. auris. This is due in part because with so few cases of the pathogen in Canada, it can be difficult for facilities to justify the upfront cost of screening programs with so many competing priorities. She hopes that surveillance efforts like these be the start of providing reliable, timely data for policy-makers and health care professionals to respond quickly to outbreaks, if and when they occur.


One way to ensure that effective antimicrobials are available when we need them in the future is to use them appropriately today. Since most antimicrobials are only available in Canada by prescription, antimicrobial prescribing is an area that can be targeted to reduce overuse of these important drugs.

A new study by a team of researchers at EPIC hospital partners provides important insights into the variabilities in antimicrobial prescribing, their consequences and possible contributors. Using data from four academic hospitals in Toronto between April 2010 and December 2019, the researchers found that the highest prescribing physicians signed off on 30% more antimicrobials than their lowest prescribing colleagues. However, despite this variability, there was no difference in patient outcomes as measured by parameters like in-hospital deaths, length of stay and hospital readmission.

These results, which were published in the Canadian Medical Association Journal, suggest that hospitals could set the amount of antimicrobials used by their lowest prescribing physicians as their stewardship target without impacting patient outcomes.

Towards the same goal, a project led by EPIC member Xiaolin Wei at the Dalla Lana School of Public Health aims to develop policy recommendations for population-level interventions to reduce inappropriate antibiotic use in primary care settings in Canada. The recommendations will be grounded in a comprehensive systematic review of the effectiveness of interventions such as public education campaigns and policies mandating prescriptions for antibiotic purchases. The recommendations will be further refined to improve their feasibility based on findings from a qualitative study of Canadian and global experiences of implementing these interventions to understand barriers and facilitators of their success.  

Infection prevention and control

An important, but less talked about, aspect of tackling AMR is efforts like vaccination and infection prevention and control (IPAC) that protect people from getting sick in the first place and reduce the need for antimicrobials.

During the COVID-19 pandemic, the Ontario Ministry of Health launched an initiative to create local IPAC hubs to share expertise with and provide support to long-term care homes and other community-based, congregate living settings. Several EPIC hospital partners were selected to lead an IPAC hub and are now well positioned to continue to help support IPAC activities beyond COVID-19 in these settings.

“The hub model allows us to extend our reach beyond hospitals into community settings where we can collaborate with our colleagues to share best practices and implement effective measures to stop the spread of harmful pathogens, including drug-resistant bacteria and fungi,” says Jennie Johnstone, an infectious diseases physician and the medical director of infection prevention and control at Sinai Health.


To ensure the success of the action plan, stakeholders from diverse sectors must come together in a coordinated way to implement the calls-to-action and work towards the target outcomes.

To that end, EPIC has created an AMR advisory group of leading researchers and health care professionals to guide the development of an AMR ecosystem. Our vision for the ecosystem is to be able to unite stakeholders across sectors and disciplines to foster collaborative research, unify advocacy and engagement efforts and drive innovation. The members of our advisory group are:

Rob BateySusy HotaLarissa MatukasMatthew MullerNicole Robbins
Leah CowenAlainna JamalKaren MaxwellJustin NodwellKevin Schwartz
Nick DanemanJennie JohnstoneAllison McGeerSamir PatelMichelle Science
Greg GermanRob KozakAndrew MorrisSusan PoutanenNicole Weckman

We are also engaging partners from academia and industry — like the AMR-One Health Consortium at the University of Calgary, bioMérieux Canada, GlaxoSmithKline and the University of Guelph — to advance the AMR cause through other initiatives. These include the second annual AMR symposium we recently co-hosted with bioMérieux Canada and the establishment of the GSK EPIC Convergence Postdoctoral Fellowship in AMR.

By working collaboratively across sectors and disciplines, EPIC and our partners are advancing innovative ideas and initiatives to meet the targets laid out in the Pan-Canadian Action Plan on AMR and address this urgent global public health threat.