Background: The southern Baltic Sea coast is an important stopover region for wild waterbirds, particularly between late August and April. These birds can contribute to the maintenance and spread of viral and bacterial pathogens, including highly pathogenic avian influenza viruses (HPAIV) and antimicrobial-resistant bacteria such as ESBL-producing Escherichia (E.) coli. The continued circulation of HPAI H5 viruses of the gs/Gd lineage has caused unprecedented global outbreaks in poultry and wild birds. While passive surveillance of sick and dead birds remains the main approach for HPAIV detection, complementary active surveillance of apparently healthy birds using simple, non-invasive sampling is needed to better understand virus ecology and evolution.

Methods: From June 2022 to December 2023, we deployed shallow plastic bins with coastal brackish water and wheat grains along the Greifswalder Bodden shore, Baltic Sea, Germany, to attract wild waterbirds. After bird visits, water samples were analyzed for influenza A virus by RT-qPCR. In July 2022, four samples were cultured for ESBL-producing E. coli.

Results: Camera monitoring confirmed that mallards (Anas platyrhynchos) were the main visitors, feeding and interacting intensively with the water. 222 water samples were analyzed for viral RNA; 13 (5.9%) were avian influenza virus-positive, including HPAI H5 (clade 2.3.4.4b) and low-pathogenic subtypes H3N8 and H11N9. All four samples yielded ESBL-producing E. coli, including one isolate of sequence type ST58.

Conclusion: This non-invasive approach is a promising tool for environmental surveillance of viral and bacterial pathogens, with sensitivity expected to improve through enrichment techniques targeting pathogens in water.