Pilot study on antimicrobial resistance monitoring in European surface waters - Final report of the Eionet Working Group

This report summarizes a pilot study conducted by the Eionet Working Group (WG) on antimicrobial resistance (AMR) monitoring in European surface waters. With AMR recognized as a major public health threat, the study aimed to develop a harmonized approach for collecting and reporting AMR data in surface waters, supporting revisions of EU water directives.

Led by the European Environment Agency (EEA) and the European Topic Centre Biodiversity and Ecosystems (ETC-BE), the WG developed methodologies and practical guidelines covering sampling, analysis, data reporting, and quality control. Sampling focused on rivers downstream of urban wastewater treatment plants (WWTPs). Target indicators included six gene markers (e.g., 16S rRNA, intl1, aadA1) via qPCR and culturing of E. coli and ESBL-producing E. coli (ESBL-Ec).

Ten of fourteen nominated countries participated, using qPCR as the main method for its cost-effectiveness. WHO’s Tricycle protocol was applied for culturing due to the absence of standardized EU methods for water. A custom data reporting template aligned with EEA’s WISE-6 model was also developed.

Results showed AMR gene abundance followed a clear gradient: WWTP inlet > outlet > downstream > upstream, consistent with previous studies. Gene removal by WWTPs ranged between 94.5%-99.9%, and ESBL-Ec levels varied between countries (0–14.5%). Wastewater treatment effectively reduced both E. coli and ESBL-Ec by over 99%.

The pilot faced challenges including funding limits, varied national capacities, and differing technical expertise. Despite this, it was viewed as a successful step toward EU-wide AMR monitoring. Priority areas for future EU-wide monitoring were identified and include defining objectives, harmonizing methods, improving QA/QC, and establishing a centralized reporting system.