One Health Surveillance for Antimicrobial Resistance and Emerging Pathogens by Targeted Metagenomics at Human-Livestock-Environment Interfaces

Viral and bacterial pathogens are ever-present risks to people and animals, as is antimicrobial resistance (AMR), which is when bacteria, viruses, fungi and parasites evolve to become resistant to the medications designed to kill them.

In Canada’s agriculture-rich Prairies, understanding the spread of pathogens among people, animals and the rest of the environment, and tracking AMR—which can be achieved by monitoring for antibiotic resistance genes (ARGs)—is crucial to the health and sustainability of all.

That’s where eDNA comes in: it can provide a more sensitive, accurate, low cost and speedy way to monitor biological systems for pathogens and ARGs. Through metagenomics (analyzing the combined genomes of multiple organisms in a sample) we can now identify pathogens and ARGs in samples from wastewater, livestock production and natural environments.

To maximize the impact of eDNA surveillance, this project will help ensure that new technologies are as cost-effective and implementable as possible for public and animal health labs, both provincially and nationally.

The “One Health” project, led by Drs. Andrew Cameron (Institute for Microbial Systems and Society at the University of Regina) and Tony Ruzzini (University of Saskatchewan), will detect the presence of human and livestock pathogens while also monitoring the presence of AMR in the environment. The team will address technical and operational questions like: Where do bottlenecks occur in sampling, extraction, sequencing and data processing? What are the limits of detection of rare species and variants? And what happens at the interface between agricultural, urban and natural environments?

The project will:

• Use targeted DNA enrichment by hybridization probe-capture sequencing (CapSeq) to combine the metagenomic benefits of detecting, genotyping and genome sequencing of pathogens with improved sensitivity and accelerated data processing compared to shotgun approaches. The project team has developed custom CapSeq probes and enrichment technologies for detecting and genotyping pathogens and antibiotic resistance in livestock, water samples, wastewater and infection diagnostics in humans and animals.
• Deploy metagenomics surveillance techniques across wastewater, water treatment and prairie wastewater, water treatment and livestock production systems, to accelerate long-term adoption of metagenomics for eDNA surveillance.
• Establish and validate eDNA and genomics operability and standards for all partners and sectors in the prairies and across Canada.