Antimicrobial resistance in surface waters — developing environmental monitoring for better risk management

Introduction

AMR is a top global public health threat recognised by the World Health Organization (WHO, 2023). The health burden from AMR infections is comparable to major diseases such as HIV and malaria, and is potentially far larger. AMR leads to infections that are getting harder to treat, resulting in prolonged illness, higher medical costs and increased mortality. Forecasts predict up to 1.9 million deaths attributable to AMR and 8.2 million associated deaths globally by 2050 (Nagavi et al., 2024). More than 35,000 people die from antibiotic-resistant infections each year in the EU, Iceland and Norway, a number that has increased in recent years (ECDC, 2025b).

The main drivers of AMR are the overprescription and improper use of antibiotics in healthcare and veterinary settings. Over time, microorganisms develop resistance against antimicrobial compounds. Discharges from hospital and urban wastewater treatment facilities can also spread antibiotic resistant bacteria and/or antibiotic resistance genes into the environment. The environment is therefore increasingly recognised as an important reservoir of AMR, potentially playing a key role in the spread of AMR.

Box 2. One Health

One Health emphasises the interconnected nature of human, animal and environmental health and advocates for a collaborative, multi-sectoral approach to address AMR (ECDC, 2025a; EEA, 2025; EFSA, 2025; WHO, 2025b).

Source: EEA, 2025.

Antibiotics and antibiotic resistant bacteria occur naturally in the environment, but can also enter through human and veterinary use, discharges from pharmaceutical industries, urban wastewater and treated sewage sludge, and agricultural manures and waste.

Natural environments can act as reservoirs for resistant microorganisms, and drive the development and selection of antibiotic resistance genes. The transfer of these genes between microorganisms is a natural process, though it can be enhanced by anthropogenic activities and factors such as pollution and temperature.

Evidence suggests that antimicrobial residues in the environment, as well as natural processes, can drive the development and spread of resistance, putting human and animal health at risk.

Figure 1. An example of a route for antibiotics and ARB to enter the environment is through agricultural manure and wastes

Alejandra Bize

EU action on AMR and the environment

The EU has taken significant actions to address AMR. This includes the Council Recommendation on stepping up EU actions to combat antimicrobial resistance in a One Health approach (EC, 2023), which extends the EU One Health Action Plan (EC, 2017). This plan contains more than 70 actions across human, animal and environmental health, and emphasises the need for robust surveillance and monitoring. Monitoring AMR in the environment is needed to understand the potential role the environment plays in driving and transmitting resistance to people and animals.

EU water-related legislation has started to address the need for AMR monitoring and reporting:

• The revised Urban Wastewater Treatment Directive (UWWTD) (EU, 2024) establishes the requirement and methodology for monitoring AMR in urban wastewater. Member States must start reporting by December 2030. An implementing act, with details of monitoring requirements, is expected in June 2026.
• Provisional agreement for revisions to the Water Framework Directive (WFD), the Environmental Quality Standards Directive and Groundwater Directive (EC, 2022) should allow indicators of AMR to be included in surface and groundwater watch lists, and the development of AMR monitoring methods.
• The Water Reuse Regulation 2020 (EU, 2020) allows AMR to be an additional requirement for water quality and monitoring within water reuse risk management plans if necessary to ensure that human, environment and animal health are adequately protected.

Relevant work includes a study from the European Food Safety Authority (EFSA) on the role the environment plays in the emergence and spread of AMR through the food chain. The study found that irrigation and surface water are of major importance (EFSA, 2021). Another study considered the impact of the use of azole fungicides, such as in pesticides, biocides and veterinary medicines, on the development of an azole-resistant fungal infection in humans (EFSA, 2025).

The EEA, together with the European Environment Information and Observation Network (Eionet) and the European Topic Centre Biodiversity and Ecosystems (ETC-BE), recently designed and conducted a pilot study to test a process to sample and analyse AMR in surface waters (Schwermer et al., 2025). In the absence of common protocols, this collaboration focused on harmonising methods, indicators, sample analysis and data reporting. These efforts contribute to the development of an integrated system for AMR surveillance in a One Health context.

AMR monitoring in the water environment

Recognising the need to monitor AMR in the environment is a relatively recent development. However, there are established mechanisms to deal with the risks posed by AMR in the food, human and animal health sectors. Taking a One Health approach means that the environment’s potential contribution should be brought in as a complement to existing surveillance. Environmental monitoring can help identify AMR hotspots; assess the spread of AMR and vectors for transmission; inform on trends and emerging genes; track the effectiveness of interventions such as waste management; and strengthen our understanding of AMR-related risks.

Revisions to the UWWTD and proposed revisions under the WFD mean that progress towards harmonised environmental AMR monitoring must be rapidly developed. An Eionet pilot study on AMR monitoring in surface waters identified several challenges to gathering robust and comparable data (Schwermer et al., 2025).

Eionet is a partnership network of the EEA and its 38 member and cooperating countries. The Eionet Working Group (WG) on AMR in surface waters, composed of experts from 14 European countries, collaborated to share knowledge, build capacity, develop and carry out a pilot study for AMR monitoring in the water environment between 2023 and 2025. National capabilities and resources varied widely. The group had several goals:  

• Developing standardised methodologies for sampling, analysis and data reporting. This included selecting indicators (both antibiotic resistance genes and bacterial), sampling locations, and analytical methods such as quantitative PCR (qPCR) and culturing techniques.
• Implementing quality assurance and control measures. Different laboratories had different analytical equipment, so the group designed a common, DNA reference material containing selected antibiotic resistance genes and bacterial indicators for calibration. To ensure data reliability and comparability, it used a universal bacterial indicator for qPCR calibration along with negative controls.
• Creating a data reporting template based on the EEA’s existing WISE-6 dataflow for water quality data. This enabled harmonised data collection and reporting to ensure comparability between countries.

Having established a harmonised, Europe-level approach to monitoring and reporting AMR in surface waters, the Eionet Working Group conducted a pilot study to test and refine the methodologies, gather data and identify challenges. The study focused on rivers downstream from urban wastewater treatment plants (UWWTP), as well as UWWTP influents and effluents.

Figure 2. River sampling for AMR monitoring

C.U. Schwermer

Key findings from the pilot study carried out by the Eionet WG on AMR in surface waters

The study made key findings related to the establishment of a harmonised monitoring system for AMR:

• Clarity and agreement on the monitoring purpose. Potential monitoring objectives in environmental AMR studies include environmental surveillance, treatment process efficacy, and public or animal health surveillance. Different purposes will drive the selection of indicator genes and bacteria, sampling locations, sampling frequency, analytical methods, etc.
• Variability in national capabilities and resources. Considerable variability existed in AMR monitoring capabilities and resources among participating countries, highlighting the need for harmonised methodologies and protocols. The level of experience with qPCR and culturing techniques varied significantly among WG members.
• Funding constraints. A lack of dedicated national funding for monitoring AMR in the environment limited activities’ scope and scale in the pilot study.
• Methodological considerations and debates. Standardising methods and protocols proved challenging. The selection of AMR indicators relevant to the monitoring objectives required extensive discussion, with debates on the relevance of certain clinical markers in environmental settings as well as the feasibility of analysis within a tight period of time.
• Quality assurance and control challenges. Harmonising sampling methods, analytical techniques, use of standards and controls, and data reporting procedures were essential to ensure results’ reliability and comparability.

Main results and conclusions from the pilot study

The WG collected water samples from UWWTPs and water bodies across ten European countries between April and December 2024. Samples were analysed for selected AMR indicator genes and two bacterial indicators (Table 1). Selected indicators were both relevant to the pilot monitoring objective and feasible for WG members to analyse on a tight timetable. They should be understood as an inspiration rather than a recommendation for future studies.  

Indicator selection focused on commonly-occurring and easily-detectable genes, along with those less abundant but clinically relevant. The bacterial indicator selection process considered indicators of faecal contamination, clinical significance, standardised protocol availability and the possible compatibility with other monitoring approaches.

Table 1. Which indicators were used during the Eionet study?

The study identified high concentrations of certain antibiotic resistance genes and antibiotic resistant bacteria in UWWTP inlets and outlets, as well as in rivers downstream of UWWTPs. The pattern of abundance was consistent with other published studies.

The abundance of monitored antibiotic resistance genes was categorised into three groups: high, intermediate and low (Figure 3). 'UWWTP inlet' showed the highest concentrations for 16S rRNA, intl1, aadA1 and ermB among the high-abundance genes. Concentrations of intl1, sul1 and tetW were higher at the 'UWWTP outlet' compared to both river sampling locations. The general trend of abundance for both gene and bacterial indicators, across sampling locations and based on median values, was 'UWWTP inlet' > 'UWWTP outlet' > 'river downstream' > 'river upstream'.

Abundance comparison between the inlet and outlet showed significant removal of several antibiotic resistance genes and antibiotic resistant bacteria of up to 99%.

Figure 3. Abundance of gene targets relative to 16S rRNA genes in samples from all WG members collected at UWWTP and river sampling locations

What is needed to monitor AMR in the water environment?

• Clearly define environmental AMR monitoring objectives to align the selection of appropriate target indicators, sampling locations, analytical methods, etc. and ensure relevant data collection.
• Harmonise methods and protocols such as sampling, analytical and reporting methodologies, to be suitable for different water types and conditions.
• Implement robust and comprehensive quality assurance and control procedures, including the use of reference materials, interlaboratory comparisons and data validation guidelines.
• Establish a centralised data reporting system to ensure efficient data collection, storage, use and integration at the national and international scale, and share with others contributing to the One Health approach. A catalogue or library of indicators is needed to ensure reported results are comparable. Reporting should align with existing surface water monitoring in Europe.
• Learn from existing initiatives and expertise in the One Health community. Significant experience in AMR among public health, veterinary and food sectors should be harnessed to support the environmental sector in scaling up monitoring in the environment.
• Promote capacity building and knowledge sharing to enhance expertise and capabilities in countries with less experience in this fast-developing area.