Zoonotic and Avian Pathogen Detections in Fecal and Sediment Samples - A Low-risk, High-throughput One Health Approach to Surveillance

This study demonstrates that a low-risk, high-throughput One Health surveillance approach using longitudinal fecal and sediment sampling in southern Manitoba effectively detects zoonotic and avian pathogens, including influenza A virus with H5 RNA, while avoiding the logistical and safety challenges associated with direct bird handling.

The Gist

Imagine trying to catch a glimpse of invisible germs that wild birds might be carrying. Usually, scientists have to chase these birds, catch them, and handle them directly to check for sickness. Think of it like trying to interview a shy, fast-moving squirrel by grabbing it mid-leap—it's tiring, risky for the researcher, and you can only catch a few squirrels before they scatter.

This paper describes a smarter, safer way to do the same job. Instead of chasing the birds, the researchers acted like detectives looking for footprints. They went to wetlands and parks in southern Manitoba, Canada, and simply collected bird poop (feces) and mud (sediment) from the ground. It's like checking the mailbox instead of waiting for the person to come to the door; you get the message without the hassle or the danger of a face-to-face encounter.

Over a five-month period in 2025, they gathered nearly 800 of these "environmental mailboxes." They then ran a high-speed check for four specific types of bird viruses: Influenza A, Newcastle disease, Avian Reovirus, and Avian Poxvirus.

Here is what their "mail" revealed:

• Influenza A: This was the most common find. About 5% of the bird poop samples had the virus, but the mud samples were much more "infected," with over 22% testing positive. Interestingly, while the mud contained a few samples with the specific H5 strain (the one that makes headlines), the bird poop samples did not.
• Newcastle Disease: This was a rare sighting, appearing in only a tiny fraction of the poop samples, and all on the very same day.
• Avian Reovirus: This showed up occasionally in the mud samples (about 7% of them) but was barely seen in the poop.
• Avian Poxvirus: After checking hundreds of samples, they found zero evidence of this virus.

The main takeaway is that this "ground-level" approach works like a wide-net fishing trip. It allows scientists to screen for many different viruses at once, covering a lot of ground without ever having to touch a wild bird. It's a low-risk, high-efficiency method that keeps both the researchers and the birds safe while still catching the viral signals hidden in the environment.

Technical Summary

Technical Summary: Zoonotic and Avian Pathogen Detections in Fecal and Sediment Samples

Problem Statement
Wild bird populations serve as reservoirs for numerous pathogens, including those with zoonotic spillover potential and avian-specific viruses. While surveillance for Influenza A viruses (IAV) is conducted annually, monitoring for other significant pathogens remains limited. Traditional surveillance methods involving the direct capture and handling of wild birds present several operational challenges: they are time-consuming, labor-intensive, restrict sample sizes, and pose direct exposure risks to personnel handling potentially infected animals. Consequently, there is a critical need for alternative surveillance strategies that mitigate these risks while maintaining efficacy.

Methodology
To address these limitations, this study employed a longitudinal, environmental sampling approach as a low-risk, high-throughput alternative to direct bird handling. Conducted from May to October 2025 in southern Manitoba, Canada (with a focus on Winnipeg), the study utilized bi-weekly collection of fecal and sediment samples. Site selection was driven by three criteria: suitability for waterfowl habitat, confirmed presence of waterfowl, and proximity to reported H5N1 influenza outbreaks.

A total of 782 combined samples were collected and screened using molecular assays for four specific targets:

• Influenza A virus (IAV)
• Newcastle disease virus (NDV)
• Avian reovirus (ARV)
• Avian poxvirus (APXV)

Subtyping was performed to detect H5 RNA specifically within IAV-positive samples.

Key Results
The study yielded the following prevalence data across the 782 samples collected:

• Influenza A Virus (IAV):
  • Fecal Samples: Out of 714 fecal samples, 34 tested positive for IAV, resulting in a prevalence of 4.8%. None of these IAV-positive fecal samples contained H5 RNA.
  • Sediment Samples: Out of 68 sediment samples, 15 tested positive for IAV, showing a significantly higher prevalence of 22.1%. Notably, four of these IAV-positive sediment samples tested positive for H5 RNA.
• Newcastle Disease Virus (NDV): Detection was minimal, with only four positive fecal samples identified (0.56% prevalence). All positive detections occurred on a single day.
• Avian Reovirus (ARV): Five positive samples were detected in sediment, representing a 7.4% prevalence rate within the sediment subset.
• Avian Poxvirus (APXV): Of the 559 samples tested to date, all results were negative.

Significance and Claims
The paper positions this work as an expansion of previous research demonstrating the utility of environmental sampling for monitoring a diverse range of avian and zoonotic pathogens. The primary significance claimed is the validation of a "One Health" surveillance framework that is both high-throughput and low-risk. By utilizing fecal and sediment sampling, the study successfully detected pathogens—including H5 RNA in sediment samples—without the logistical burdens and safety hazards associated with physically handling wild birds. The findings support the adoption of environmental sampling as a viable, efficient complement to traditional surveillance methods.