What wastewater can tell us about antimicrobial resistance
Wastewater can provide a population-level view of antimicrobial resistance. With new European requirements putting wastewater AMR monitoring on the agenda, the question is becoming increasingly practical: how do we turn a complex sample into information that public health systems can use?
Every day, wastewater collects biological material from entire communities. That makes it an unusual surveillance sample. Instead of testing one patient or one isolate at a time, wastewater can provide information about antimicrobial resistance (AMR) across the population contributing to a wastewater catchment [1,2]. The COVID-19 pandemic brought wastewater surveillance into much wider use. The infrastructure and experience built during that period have since prompted researchers and public health authorities to investigate what else we can learn from sewage. AMR is increasingly part of that conversation [2,3].
1. A different view of antimicrobial resistance
AMR surveillance has traditionally relied heavily on clinical samples and cultured isolates. These remain essential for understanding resistance in individual pathogens and informing patient care. Resistant microorganisms and AMR genes, however, also circulate between humans, animals and the environment [3,4]. Wastewater sits at an interesting point between these systems. Municipal wastewater receives biological material from large human populations, while wastewater from hospitals and other settings can contribute additional resistance signals.
This makes wastewater relevant to a One Health approach to AMR surveillance, where information from human, animal and environmental sources contributes to our understanding of how resistance circulates [3]. It also gives researchers access to a different type of sample. Clinical surveillance depends on people interacting with healthcare systems and suitable specimens being collected. Wastewater provides an aggregated sample from the population contributing to a catchment [1].
Monitoring AMR genes or resistant bacteria in these samples over time can help researchers examine changes in resistance patterns and compare geographical areas. We are already seeing this tested at scale: a 2024 study in Wales analysed weekly wastewater samples from 47 wastewater treatment plants, comparing high-throughput qPCR targeting 73 resistance genes with metagenomic sequencing [5]. The work demonstrated the feasibility of examining AMR patterns through wastewater at national scale, while showing how targeted molecular methods and sequencing can provide different layers of information.
2. What wastewater cannot tell us on its own
Wastewater is also a complex sample. Its composition changes between locations and over time. Targets may occur at low concentrations, and the matrix itself can complicate downstream molecular analysis. Interpretation matters too. Detecting an AMR gene does not automatically tell us which organism carries it, whether that organism is viable or what clinical risk the finding represents [1,4].
The method therefore needs to match the surveillance question. Culture-based approaches can provide phenotypic information. Metagenomic and whole genome sequencing can provide deeper characterization of organisms and resistance determinants. Targeted molecular methods such as PCR and LAMP can efficiently screen samples for defined resistance markers [2,5]. These methods can work at different points within the same surveillance system.
3. Europe is moving towards routine AMR wastewater surveillance
The regulatory context is now changing too. The recast EU Urban Wastewater Treatment Directive (EU) 2024/3019 introduces wastewater surveillance into the European framework for urban wastewater management [6]. Under Article 17, Member States must establish national systems for cooperation and coordination between public health authorities and the authorities responsible for urban wastewater treatment.
The Directive goes further for AMR. For agglomerations of 100,000 population equivalent and above, Member States will be required to ensure that antimicrobial resistance is monitored in urban wastewater according to the timeline established by the Directive and the corresponding implementing act [6]. The legislation also provides for a minimum sampling frequency and a harmonised methodology for measuring AMR [6].
WHO has reached a similar point from the public health perspective. Its 2025 AMR-specific wastewater surveillance summary describes wastewater and environmental surveillance for AMR as technically and operationally feasible, while noting that it has yet to enter widespread routine use [4].
Together, these developments shift the conversation. The scientific question of whether wastewater can provide useful AMR information is increasingly being joined by a practical one: how can surveillance be implemented consistently across many locations?
Laboratory capacity is part of that equation. Sequencing can provide rich information, but routine implementation requires suitable infrastructure, specialist expertise and bioinformatics capacity. Access to those resources varies considerably between surveillance settings [2].
Targeted molecular testing provides another route. When the objective is to determine whether selected resistance markers are present, PCR-based assays can screen defined genes without requiring every sample to proceed immediately to deeper genomic characterization [2,5]. Findings that warrant further investigation can then be examined using culture, sequencing or other reference methods. This creates the possibility of a tiered surveillance model: broader targeted screening across multiple locations, combined with deeper characterization where it adds the most information.
And as European countries build wastewater AMR monitoring into their surveillance systems, repeatable sample processing and molecular workflows will become an increasingly practical consideration.
This is one of the questions we have been working on at Invitek Diagnostics. Our upcoming InviDx® platform is being developed for decentralized molecular screening of antimicrobial resistance markers across different One Health sample contexts. Wastewater is one potential application.
The concept is to enable targeted screening for selected AMR markers closer to where surveillance takes place. Results could contribute one layer of information within a wider surveillance programme, while samples or findings requiring deeper characterization could proceed to culture, sequencing or reference laboratory analysis. The same principle can extend across human health, animal health, food and environmental surveillance. That matters because resistance does not stay within the boundaries of any one of those sectors.
Wastewater gives us access to something difficult to obtain through individual clinical samples alone: a recurring, population-level sample of the microbial signals passing through a community. There are still open questions around sampling, normalization, analytical methods and interpretation [1,2,4]. But the direction is becoming clearer. WHO is developing wastewater surveillance as part of broader public health surveillance, while Europe is putting the regulatory framework for AMR wastewater monitoring in place [4,6].
During World Water Week, there is a good reason to look at wastewater from another angle. Alongside asking which pathogens are circulating, we can increasingly ask: what resistance is circulating with them?
[1] Chau KK, Barker L, Budgell EP, et al. Systematic review of wastewater surveillance of antimicrobial resistance in human populations. Environ Int. 2022;162:107171. doi:10.1016/j.envint.2022.107171.
[2] Malcom HB, Bowes DA. Use of wastewater to monitor antimicrobial resistance trends in communities and implications for wastewater-based epidemiology: a review of the recent literature. Microorganisms. 2025;13(9):2073. doi:10.3390/microorganisms13092073.
[3] Punch R, Azani R, Ellison C, et al. The surveillance of antimicrobial resistance in wastewater from a One Health perspective: a global scoping and temporal review (2014–2024). One Health. 2025;21:101139. doi:10.1016/j.onehlt.2025.101139.
[4] World Health Organization. Wastewater and Environmental Surveillance: Summary for Antimicrobial Resistance. Pilot version. Geneva: World Health Organization; 2025
[5] Knight ME, Webster G, Perry WB, et al. National-scale antimicrobial resistance surveillance in wastewater: a comparative analysis of HT qPCR and metagenomic approaches. Water Res. 2024;262:121989. doi:10.1016/j.watres.2024.121989.
[6] European Parliament and Council of the European Union. Directive (EU) 2024/3019 of the European Parliament and of the Council of 27 November 2024 concerning urban wastewater treatment (recast). Official Journal of the European Union. 2024.