Testing wastewater for public health

This "Cookbook" provides a comprehensive strategic and technical framework for implementing wastewater-based surveillance (WBS) through metagenomic analysis as a tool for early detection of infectious diseases, antimicrobial resistance (AMR), and emerging public-health threats. It proposes a dual-track surveillance model that combines non-target (shotgun) metagenomics for unbiased discovery of novel or unexpected pathogens with targeted metagenomics for rapid detection and monitoring of high-priority pathogens, viruses, bacteria, and AMR markers. The framework outlines evidence-based approaches for pathogen and AMR prioritisation, including the use of multicriteria decision analysis (MCDA) to evaluate public-health impact, feasibility, cost, and data availability. It presents end-to-end technical workflows covering wastewater sampling, nucleic-acid extraction, sequencing across major platforms, and bioinformatic pipelines for taxonomic and functional characterisation. In addition, the guide emphasises integration with clinical and syndromic surveillance systems within a One Health framework to improve situational awareness, outbreak preparedness, and early-warning capacity. The cookbook also addresses key aspects of data governance and ethics, including compliance with privacy regulations, mitigation of community-level risks, implementation of FAIR data principles, and the application of differential privacy approaches where appropriate. Operational considerations such as quality assurance and control (QA/QC), laboratory standardisation, workforce training, scalability, transparency, reproducibility, and international collaboration are presented as essential components for sustainable deployment. Drawing on state-of-the-art advances from global WBS programmes, WHO guidance, and peer-reviewed scientific literature, the guide provides a high-level yet practical best-practice resource for practitioners, laboratories, and public-health operators seeking scalable and adaptable surveillance systems. While promoting harmonised methodologies and international cooperation, it recognises the need for flexibility according to local epidemiology, infrastructure, resources, and innovation. Ultimately, the framework aims to strengthen wastewater intelligence as a core element of global health security, enabling earlier detection of zoonotic threats, resistance patterns, and outbreaks while supporting evidence-based policy-making and multi-sectoral resilience.

COMERO Sara;  GLOWACKA Natalia;  PANZARELLA Giulia;  TAVAZZI Simona;  ETHELBERG Steen;  FRIEDMAN Cindy R.;  TESSEMA Sofonias Kifle;  YOUSIF Mukhlid;  MARX Gernot;  KLEIN Christophe;  PETRILLO Mauro;  LOESCHNER Jan;  ROSINSKA Anna;  PIERANNUNZI Francesco;  BAUSA LOPEZ Luis;  SION Sorin;  KOUTSOLIOUTSOU Anastasia;  ALPASLAN KOCAMEMI Bilge;  GAWLIK Bernd Manfred; 

2026-06-24

Publications Office of the European Union

JRC147000

978-92-68-40922-0 (online),   

1831-9424 (online),   

EUR 40762,    OP KJ-01-26-268-EN-N (online),   

https://publications.jrc.ec.europa.eu/repository/handle/JRC147000,   

10.2760/4141191 (online),