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Genomics-based pathogen surveillance

Strategic initiative

Rising to the challenge

Genome Canada is deeply committed to genomic surveillance due to our pivotal role in advancing public health, understanding disease dynamics and bolstering biosecurity. By harnessing the power of genomic sequencing technologies, we aim to support the systematic monitoring and analysis of genetic information from pathogens, organisms and populations. This proactive approach enables the timely detection of emerging infectious diseases, the tracking of disease spread within communities, and the identification of genetic factors influencing disease susceptibility and treatment outcomes.

Genomic surveillance also enhances our ability to respond effectively to disease outbreaks, develop targeted interventions and inform policy decisions for better health outcomes. Through our dedication to genomic surveillance, we strive to contribute significantly to the advancement of scientific knowledge, public health preparedness and the protection of global health security.

Genomic surveillance is the consistent monitoring of pathogens, and analysis, via genome sequencing, of their genetic similarities and differences. This method uses genomic sequencing technologies to monitor changes in genetic material over time, offering valuable insights into the evolution, transmission and traits of different biological entities.

The World Health Organization (WHO) has identified the need for coordinated and inclusive access to genomic surveillance through its 10-year Global Genomic Surveillance Strategy. And genomic surveillance 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. 

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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 monitoring 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 monitoring 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 monitoring 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
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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

Leading-edge pandemic preparedness

Evidence-informed decision making for healthier communities, wildlife and ecosystems

Equitable access to genomic monitoring across Canada


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

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

Regional EP and AMR monitoring teams

Approx. $6M

Six regional teams will be funded to implement monitoring 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

in federal investment through
Genome Canada to kick-start the initiative
$ 0 M
for community collaboration
and coordination (C3 Hub)
$ 0 M
for regional EP and AMR
monitoring teams
$ 0 M
for Indigenous-led monitoring
in northern and remote communities
$ 0 M
co-funding ratio required for
regional monitoring teams and C3 Hub
1: 1


Contact Genome Canada:

Or contact a regional Genome Centre directly. Genome Centre contacts are listed in each funding opportunity.