Monitoring of antimicrobial resistance genes and influenza viruses in avian-populated water bodies

Monitoring zoonotic and multi-species pathogens is challenging due to the resources required to sample individual animals. In this study, we propose the use of DNA/RNA detection methods to assess the prevalence of bacterial, antimicrobial resistance (AMR), and viral markers in 19 water sites in England and Wales where close contact occurs with avian species. For bacteria and AMR monitoring, we utilised high-throughput quantitative PCR (HT-qPCR), which revealed a consistent abundance of AMR genes and mobile genetic elements, with aminoglycoside-resistance gene aadA7 being most prevalent. Elevated levels of multidrug resistance genes were detected at two sites, potentially linked to wildlife rather than anthropogenic factors. The intl3 gene was a dominant integron, supporting its use as a marker for AMR prevalence. We also developed a streamlined pipeline (including sampling, sample process and pathogen identification/quantification) for influenza prevalence assessment. The detection of influenza virus coincided with reported avian influenza outbreak in wild birds. The frequent detection of human (crAssphage) and bird-associated (Catellicoccus marimammalium) markers suggested that they provide a robust framework for assessing faecal pollution in water bodies. This study demonstrates how molecular monitoring can track emerging pathogens simultaneously and identify pollution sources, providing a valuable approach for the surveillance of zoonotic threats.