Prairie pond located near Mankota, Saskatchewan. Photo credit: Emily Lightheart.
Across the Canadian Prairies, agriculture, communities, and natural ecosystems are closely connected. Rivers run through farmland, livestock operations sit near wetlands, and wildlife moves freely across vast landscapes. These shared spaces support the region’s economy and way of life—but they also create pathways through which viruses and bacteria can move between animals, people, and the environment.
FEATURE ARTICLE
Understanding how pathogens travel through these interconnected systems has long been a challenge for scientists and public health officials. A new research initiative is working to shed light on these hidden pathways by using an emerging tool known as environmental DNA, or eDNA.
By studying tiny traces of genetic material found in the environment, researchers hope to build a clearer picture of where disease-causing microbes and antibiotic-resistant genes exist, how they move through Prairie ecosystems, and where potential risks may emerge in the future.
Launched in late 2025, The Environmental DNA Surveillance Initiative (or eDNA Surveillance Project) seeks to develop practical tools that can monitor pathogens across agricultural systems, communities, and natural landscapes. The $1.83 million project with $475,000 in supports from Genome Canada, is co-led by Dr. Andrew Cameron, a microbial geneticist at the University of Regina, and Dr. Tony Ruzzini, Associate Professor at the Department of Veterinary Microbiology at the University of Saskatchewan.
Understanding a Shared Health Landscape
In recent years, scientists have increasingly recognized that human health, animal health, and environmental health are closely linked. Diseases that affect people sometimes originate in animals. Similarly, bacteria that develop antibiotic resistance in agricultural settings can potentially spread through water systems or other environmental pathways.
To address these connections, researchers use the concept of “One Health.” The approach recognizes that protecting human health requires understanding the broader ecosystems in which people live.
“The things that infect humans can be the same things that infect what we eat like cattle or chickens or various animals that we share the environment with,” said Cameron. “The project is based on understanding the interconnectedness between humans, animals and environments – particularly the transmission of pathogens and ongoing challenges like antimicrobial [antibiotic] resistance.”
On the Prairies, those interconnections are especially prominent. The region is home to large livestock populations and extensive agricultural production. At the same time, it has relatively small human populations spread across large geographic areas. Rivers, wetlands, and agricultural drainage systems connect these environments in complex ways.
“The Prairie region is unique,” Cameron says. “It’s sparsely populated with humans but it also has a huge area of agricultural activity and livestock population. Understanding how pathogens move across those systems is incredibly important.”
Project researchers take samples from a creek within the Fort McPherson district in The North West Territories. Photo credit: Laura Schnell.
A New Way to Detect Pathogens
For decades, disease surveillance has largely focused on clinical settings. Doctors test patients for infections, and veterinarians test animals when illness appears in herds or flocks. While these approaches remain essential, they typically detect problems after they have already begun to spread.
Environmental DNA offers a way to look for pathogens much earlier.
Every living organism, from bacteria to animals, leave behind tiny fragments of genetic material in its surroundings. These traces can be found in water, soil, or even air. By collecting environmental samples and analyzing the DNA they contain, scientists can detect organisms that may be present in extremely small numbers.
eDNA has been used in recent years for tasks such as monitoring endangered species or detecting invasive fish in lakes. Now researchers are adapting it to track pathogens and antibiotic resistance genes across large environments.
This is no small challenge. In most samples, disease-causing microbes make up only a tiny fraction of all biological material. However, advances in DNA sequencing technology now allow scientists to scan millions of genetic fragments at once. That capability makes it possible to identify pathogens even when they are buried within a vast amount of other biological material.
“eDNA is the probably most sensitive approach we have to detect any biological form,” Cameron said. “It means we can use the biological components that are shared by all living and nonliving things, including viruses, and detect them with incredibly high sensitivity.”
Among other sampling strategies, the eDNA Surveillance Project examines how runoff in rural water sources such as this pond located naer Southey, Saskatchewan, are affected. Photo credit: Laura Schnell.
Integrating Many Different Environments
One of the most distinctive aspects of the eDNA Surveillance Project is its scope. Instead of focusing on a single environment, researchers are combining information from many different systems.
Samples may come from agricultural settings such as cattle feedlots, from wastewater treatment systems in urban areas, or from natural environments such as rivers and sediments. All of these samples are analyzed using a common platform designed to detect pathogens and antibiotic resistance genes.
“The project integrates samples from many different systems including areas like livestock, agricultural and human health systems,” said Ruzzini. “The project funnels different sample types from each system into a common platform for the detection of pathogens, and antimicrobial resistance genes.”
Each environment has its own unique characteristics. For example, pathogens found in livestock operations may differ from those found in hospitals or municipal wastewater systems. However, analyzing them together allows scientists to see patterns that might otherwise go unnoticed.
“We can tailor the methods for specific environments when needed,” Ruzzini explains. “But utilizing a common platform allows us to compare across systems and learn how pathogens might be moving between them.”
Water samples taken from one of the countless prairie region water sources, pictured here is a pond in Vibank, Saskatchewan. Photo credit: Laura Schnell.
Searching for Hidden Reservoirs
A key focus of the research is understanding antimicrobial resistance (or AMR).
Antibiotics have transformed modern medicine by allowing doctors and veterinarians to treat bacterial infections effectively. However, over time, some bacteria develop resistance to these drugs. When that happens, infections can become much harder to treat.
Antimicrobial-resistant bacteria are not limited to hospitals. They also appear in agricultural environments, wastewater systems, and natural ecosystems. Importantly, bacteria readily share the genes with other microbes in the environment to increase the rise of AMR.
While regulators in Canada have recently introduced stricter controls on antimicrobial use in agriculture, livestock populations still receive significant amounts of antibiotics for disease prevention and treatment. Scientists want to better understand where resistance genes might be present outside clinical settings.
“Where do antimicrobial resistance genes spread and persist outside of hospitals?” Cameron asks. “How long do they reside in sediments? In water systems? In agricultural environments?”
By analyzing environmental DNA from a variety of locations, researchers hope to identify potential reservoirs of resistance genes and better understand how they spread and evolve.
The area examined in the project is vast – from Saskatchewan to Manitoba to the North West Territories, to (pictured above) Inuvik Territory. Photo credit: Laura Schnell.
Moving from Reaction to Prevention
The COVID-19 pandemic highlighted the importance of disease surveillance systems. Wastewater monitoring programs, for example, became valuable tools for tracking the spread of SARS-CoV-2 in communities.
Projects like the Prairie eDNA initiative aim to expand that concept by creating broader monitoring networks that can detect multiple pathogens across many environments.
Traditionally, surveillance efforts have often focused on responding to outbreaks once they occur. Environmental DNA could help shift that model toward prevention.
Over time, that knowledge could help identify early warning signs of emerging threats. For example, if certain pathogens begin appearing more frequently in specific environments, health officials could intervene before large outbreaks occur.
“Surveillance helps us build baseline data,” Cameron explains. “Not only do we keep improving technologies, we gain baseline data of how different pathogens move through the myriad systems on the prairies and where the risks lie.”
“It means we can see where pathogens are evolving, where new pathogens emerge, and where antimicrobial resistance genes may be residing when they’re not in the human clinical settings.”
Environmental sampling may also reveal locations that serve as useful long-term monitoring sites.
“By sampling different environments, we might get clues about the best places to look for problematic genes,” Ruzzini says. “That information can help inform better surveillance strategies in the future.”
FOR MORE INFORMATION ABOUT THIS ARTICLE PLEASE CONTACT
Tony Bassett
Director of Communications
Genome Prairie
text/voice: 306.881.0255
email: tbassett@genomeprairie.ca
