Study of water bodies frequented by wild birds reveals presence of antimicrobial resistance genes in nine in 10 samples

The first UK study to monitor antimicrobial resistance and influenza viruses in water bodies has revealed that 92% of samples contained genes for resistance to colistin, an antibiotic of last resort.

The study, ‘Monitoring of antimicrobial resistance genes and influenza viruses in avian-populated water bodies’ was carried out by researchers at Bangor University and was published in Sustainable Microbiology, an Applied Microbiology International publication.

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“Our research group at Bangor University conducted the first study in the UK to monitor the presence of antimicrobial resistance and influenza viruses (both often originate from wildbirds) in water bodies in England and Wales in 2023-24. Our goal was to develop sustainable, non-invasive methods for tracking zoonotic threats in environments often visited by people and also frequented by birds, especially migratory species, which can be vectors for disease transmission,” said corresponding author Dr Kata Farkas.

Global concern

The study was designed to address the growing global concern of zoonotic disease transmission and antimicrobial resistance, both of which pose serious threats to public and animal health. Traditional surveillance methods rely on testing sick or dead animals, which is sporadic, resource-intensive and reactive, so the team aimed to find a more proactive, scalable, and sustainable approach to monitor emerging pathogens—particularly AMR bacteria and avian influenza viruses—by analysing environmental water samples instead of individual animals.

Water samples were collected weekly from 19 sites including inland and coastal water bodies, over a 10-week period, with additional long-term sampling at four sites.

High-throughput quantitative PCR (HT-qPCR) was used to detect 74 AMR genes, mobile genetic elements (MGEs), and bacterial taxonomic markers.

Influenza virus detection was performed using RT-qPCR to detect influenza A and B typed viruses and subtyping was attempted using end-point PCR.

Molecular markers and source tracking

The research team also explored the potential origin of microbial contamination in water utilising molecular marker quantification using qPCR. CrAssphage is a bacteriophage specific to the human gut and hence its gene segments have been used as a human-specific marker. 

Meanwhile, the bacterium Catellicoccus marimammalium is found in the gut of many wild birds (mainly gulls and pigeons) and sea mammals and hence an ideal marker for coastal-avian contamination.

Faecal markers revealed mixed contamination sources, with bird-associated markers more prevalent than human ones.

AMR and pathogens

The study found that AMR genes were widespread, with the aminoglycoside-resistance gene aadA7 being the most prevalent. Multidrug resistance genes were notably elevated at two sites, possibly due to wildlife rather than human activity.

“The high prevalence of the mcr1 gene (conferring resistance to colistin, a last-resort antibiotic) in 92% of samples was unexpected,” Dr Farkas said. “The frequent detection of Shigella spp. DNA, despite the absence of other common bacteria like E. coli and enterococci, was surprising and may reflect limitations in detection sensitivity of the HT-qPCR assay. 

Influenza A virus was detected in 3.4% of samples, with no subtypes (like H5N1) found, most likely due to the low levels of viruses in the samples. “Influenza virus RNA was detected even in the absence of reported outbreaks, suggesting possible human sewage contamination.”

Powerful tool

This study demonstrated that environmental DNA/RNA monitoring can be a powerful tool for early detection of any zoonotic threats, offering a cost-effective and scalable alternative to traditional animal testing, Dr Farkas said. 

“It supports the One Health approach by integrating environmental, animal, and human health surveillance. The findings also highlight the role of birds in spreading AMR and the potential for environmental water bodies to act as reservoirs or indicators of emerging public health risks. 

“Further, it also supports the monitoring of human and animal-derived markers to determine the origin of faecal contamination in water, which is not possible using the current regulatory monitoring, which relies on detecting bacteria that can originate from both human and animal sources. 

“qPCR-based assays can be developed and validated over a short period of time, so any emerging health threats and novel markers can be easily incorporated in DNA/RNA monitoring schemes.”

Broader monitoring

Next steps should include broader and longer-term monitoring to capture seasonal and regional trends in AMR and influenza prevalence, she said.

“The development of more sensitive PCR- or sequencing-based methods to subtype influenza viruses in low-concentration samples would also be beneficial for a more comprehensive assessment.

“The long-term goal is to incorporate environmental monitoring into national disease surveillance frameworks to enhance preparedness for future outbreaks and pandemics.”

The study was led by Bangor University and funded by the UK Health Security Agency (UKHSA). UKHSA and the British Trust for Ornithology contributed to site selection.

‘Monitoring of antimicrobial resistance genes and influenza viruses in avian-populated water bodies’ is published in Sustainable Microbiology.