Genomic Monitoring of Pathogens in Water

Strategic initiative

FUNDING OVERVIEW 

Rising to the challenge

The Genomic Monitoring of Pathogens in Water (GeMPaW) initiative, launched in April 2023 with a $10 million Genome Canada investment, will help Canada defend its population, wildlife and environment from major threats posed by emerging pathogens (EPs) and antimicrobial resistance (AMR), including antibiotic resistant bacteria and genes. Through cutting-edge genomic ­­­­monitoring in water and pan-Canadian collaboration, this strategic initiative will prepare Canada for future pandemics and other emerging health challenges with a One Health approach.

What is genomic monitoring/surveillance?

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.

Why this issue matters now

The World Health Organization (WHO) has identified the need for coordinated and inclusive access to genomic monitoring through its 10-year Global Genomic Surveillance Strategy. And genomic monitoring strategies across the world are evolving toward more collaborative, effective and cost-efficient approaches, like those enabled by water sampling and genome sequencing. The WHO has also highlighted the growing threat of antimicrobial resistance (AMR) caused by the antimicrobials used to fight infection in its Global Action Plan on Antimicrobial Resistance. The Government of Canada launched a pan-Canadian framework—led by the Public Health Agency of Canada—to support and implement the WHO’s global plan, and to deploy a made-in-Canada plan to address the issue.

In response to these major challenges, Genome Canada’s latest initiative will support Canada’s response to emerging and antimicrobial resistant pathogens through strategic investments in genomic monitoring in water. This will build on the Genome Canada-led Canadian COVID-19 Genomics Network (CanCOGeN) and existing federal efforts by using applied genomic monitoring data to inform public health and policy decisions in Canada.

The challenge

Emerging infectious diseases—which are mostly transmitted between animals and humans, as with Zika, Ebola, mpox (monkeypox) and COVID-19—are becoming more prevalent and an increasing threat to global health. 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 also key to tackling antimicrobial resistance (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 hotspots, for example.

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

The solution

The Genomic Monitoring of Pathogens in Water 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 initiative will invest in an integrated portfolio of projects building regional capacity and national alignment to tackle EPs/AMR through:

-      Community coordination and collaboration (the C3 Hub)

-      Regional monitoring for EPs and AMR

-      Indigenous-led monitoring in northern and remote communities

One Health approach

EPs and 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 crop yields and reduce infection. Given the connected nature of our world, a One Health approach to genomic monitoring, considering threats to humans, animals and the environment, is key to tackling them. This initiative will bring together diverse partners to improve integration and alignment of different genomic monitoring systems in Canada across research areas—advancing our understanding of the connections between people, animals, plants and their shared environments.

Complex challenges require strategic solutions delivered by diverse and engaged stakeholders. Coordinating the efforts of a broad range of partners in Canada’s genomics ecosystem around this shared challenge will deliver significant impact for communities across the country.

Translating genomics solutions into impact for Canada

Programs

Three programs will drive the Genomic Monitoring of Pathogens in Water initiative.

Funding Overview 

Community Coordination and Collaboration Hub (C3 Hub)
Approx. $3M

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

Launched April 26, 2023

Funding opportunity

Regional EP and AMR monitoring teams

Approx. $6M

Six regional teams will be funded to implement surveillance programs for emerging pathogens (EPs) and antimicrobial resistance (AMR) in water. 1:1 co-funding, up to $1M available per Genome Centre

To be launched in winter 2024

Indigenous-led monitoring in northern and remote communities

Approx. $1M

Genomic monitoring projects in northern and remote communities that are led by community-based Indigenous researchers and/or organizations, take place on Indigenous land or incorporate Indigenous knowledge. Co-funding not required

Launch date TBC.

By the numbers

$10M - in federal investment through Genome Canada to kick-start the initiative

$3M - for community collaboration and coordination (C3 Hub)

$6M - for regional EP and AMR monitoring teams

$1M - for Indigenous-led monitoring in northern and remote communities

1:1 -co-funding ratio required for regional monitoring teams and C3 Hub

Contact

Contact Genome Canada at gempaw@genomecanada.ca. or Genome Alberta at info@genomealberta.ca