Genomic Monitoring of Pathogens in Water (GeMPaW)

Please note: Interested applicants are strongly encouraged to contact Genome Prairie (contact info below) as the process requires registration with the federal funding agency, Genome Canada.

The Challenge

Emergent pathogens (EPs) and antimicrobial resistance (AMR) are a rising threat to all sectors of the ecosystem: humans, animals and the environment. Importantly, antimicrobial agents aren’t just used for human health. They are also used throughout the food chain — including in agriculture and fisheries, to improve yields and reduce infection. The GeMPaW initiative will bring together diverse partners to improve integration and alignment of different genomic monitoring systems across the research areas – advancing our understanding of the connections between people, animals, plants and their shared environments.

Rising to the Challenge:

Genomic monitoring (or “genomic surveillance” as it is commonly referred to) is the consistent monitoring of pathogens, and analysis, via genome sequencing, of their genetic similarities and differences. This includes water-based monitoring, which uses genome sequencing to test for pathogens in water sources, such as sewage, wastewater treatment plants, saltwater, freshwater and groundwater. During the COVID-19 pandemic, for example, genome sequencing of unprocessed sewage samples emerged as a practical, low-cost solution for monitoring the virus.

The Genomic Monitoring of Pathogens in Water (GeMPaW) strategic initiative will scale-up genomic surveillance of emerging and antimicrobial resistant pathogens in water—driving adoption of best practices for water testing, data sharing and pan-Canadian collaboration to inform public decision making. It will also build operational structures and integrated processes to support genomic surveillance efforts across the country.

The GeMPaW initiative will invest in an integrated portfolio of projects building regional capacity and national alignment to tackle EPs and AMR through three funding opportunities:

·         1 – Community coordination and collaboration (the C3 Hub)

·         2 – Regional monitoring for EPs and AMR

·         3 – Indigenous-led monitoring in northern and remote communities

Why This Matters:

Emerging pathogens are newly discovered or previously unknown infectious agents that have recently appeared or are increasing in incidence, and pose a threat to public health due to their ability to cause disease in humans. Early genomic monitoring of the pathogens that cause these diseases is crucial to keeping communities, wildlife and the environment healthy.

Expanding water-based genomic monitoring has enormous potential to transform Canada’s preparedness for, and response to, other pathogens.

Genomics is key to tackling AMR which occurs when pathogens evolve mechanisms that reduce the effectiveness of antimicrobial medicines used to treat infection. Globally, AMR is associated with 4.95 million human deaths per year and directly attributed to at least 1.27 million more. By some estimates, AMR may cause more deaths than cancer by the year 2050.

Water-based surveillance promises to deliver crucial tools for AMR mitigation. These could include assessment of the antibiotic resistance genes that circulate among human populations, and identification of antimicrobial resistance hot spots.

While there is significant potential for water-based genomic monitoring, Canada faces big challenges in harnessing it. To achieve success, we must eliminate silos preventing pan-Canadian coordination to detect and report pathogens by implementing uniform standards, harmonization of techniques and sharing of the data generated by genomic sequencing of water samples.


This is an ongoing process. Potential applicants are encouraged to contact Genome Prairie prior to starting the application process. Registration deadline for individuals in the C3 Hub, is 04:30 p.m., Wednesday, May 31, 2023.

The Funding Opportunities:

Community Coordination
and Collaboration Hub (C3 Hub)

Funding: Up to $3M
Launched: April 26, 2023

The C3 Hub will act broadly as connector, ensuring that water-based pathogen and AMR
genomic monitoring data are used to inform public policy decisions. 1:1 co-funding required.

Regional EP and AMR Monitoring Teams
Funding: Up to $1M
Launch: Autumn, 2023

Six regional teams will be funded to implement surveillance programs for emerging pathogens
(EPs) and antimicrobial resistance (AMR) in water. 1:1 co-funding.

Indigenous-Led Monitoring in Northern and Remote Communities
Funding Amount: Up to $1M
Launch: TBD

Funding Initiative Documents:


For more information about this funding initiative, please contact Dr. Lester Young, Chief Scientific Officer, Genome Prairie at