Wastewater could become an early warning system for antibiotic resistance

Monitoring of wastewater could be used for early detection and tracking of the spread of antimicrobial resistance, one of the main global health threats, according to a scientific analysis presented by the European Commission's Directorate-General for Environment. The method allows for the identification of genes that confer antibiotic resistance to bacteria in sewage samples and could indicate where local outbreaks occur, how resistance circulates between communities, and what health, social, and environmental factors facilitate its spread.

In short, wastewater monitoring, widely used for tracking COVID-19, could be expanded for the detection of genes associated with antimicrobial resistance and for the rapid identification of high-risk areas. The analysis shows links between the abundance and diversity of these genes and factors such as sewage infrastructure, access to clean water, antibiotic pollution, and socioeconomic and health conditions. The system can be applied from the level of a single building to entire cities and can monitor sources such as hospitals, farms, pharmaceutical factories, and municipal sewage networks. Large-scale implementation requires advanced genetic sequencing, standardized sampling, comparable analysis between regions, and clear rules regarding confidentiality and data sharing. The research recommends integrating wastewater monitoring into the One Health approach, which addresses the health of people, animals, and ecosystems within a single framework and is already one of the EU's directions for combating antimicrobial resistance.

Antimicrobial resistance occurs when microorganisms no longer respond effectively to the drugs used against them. In the case of bacteria, this can make antibiotics less effective or unusable, turning treatable infections into much harder-to-control medical problems. The analysis presented by the Commission indicates an estimate that antimicrobial resistance could be associated with approximately 1.91 million deaths annually worldwide by 2050.

One of the major difficulties in combating this phenomenon is that the emergence and spread of resistance do not occur exclusively in hospitals. Bacteria and resistance genes circulate among humans, animals, and the surrounding environment through water, food, farms, waste, sewage, and various economic activities, making it difficult to observe the phenomenon through medical surveillance systems focused only on patients.

Wastewater-based monitoring offers a possibility to observe a larger part of this circuit. Samples collected from sewage contain biological material from a large number of people and different sources, and genetic analysis can detect the genes that allow microorganisms to resist certain antibiotics.

The method became known to the public during the COVID-19 pandemic when wastewater analysis was used to detect the circulation of the virus in communities before all cases were individually diagnosed. The research now analyzed supports that the same infrastructure and experience can be adapted for antimicrobial resistance, although the genetic problem is more complex than tracking a single virus.

Instead of detecting a specific pathogen, antimicrobial resistance surveillance involves identifying a very large number of genes and the combinations in which they appear. Antibiotic resistance genes can circulate among different microorganisms and can transfer to new genetic hosts, complicating risk assessment and interpretation of results.

The analysis cited by DG Environment identifies 49 resistance genes that have been repeatedly detected in different environments and distinct geographical regions. Their widespread presence suggests both the possibility of persistent local circulation and the capacity for international spread.

The distribution of these genes is not uniform. The studies analyzed show strong associations between the quantity and diversity of resistance genes and the socioeconomic, health, and environmental conditions of communities. Sewage infrastructure, access to clean water, the quality of medical services, and the level of antibiotic pollution can influence the resistance profile identified in wastewater.

Monitoring could thus become more than just a tool for measuring an existing problem. Repeated and standardized use of samples could allow for the identification of changes over time and the detection of the emergence of new genes or the rapid increase of already known forms of resistance.

Such a signal could be used for local interventions. In a region where an unusually high concentration of a particular form of resistance is identified, health authorities could investigate the source, and the information could contribute to decisions regarding antibiotic prescribing or measures to limit the spread.

Monitoring can be conducted at very different scales. A sample can represent a single building, a hospital, a farm, an industrial facility, a neighborhood, or an entire city, depending on the point in the sewage network where it is collected.

This flexibility also allows for differentiation of sources. Wastewater from a hospital may reflect intensive antibiotic use and the circulation of resistant microorganisms associated with the medical environment, while samples from farms may show different genetic profiles influenced by the use of antimicrobials in veterinary medicine.

Pharmaceutical facilities represent another possible source. The release of antibiotics or their residues into water can create selection pressure on environmental microorganisms and can promote the development and maintenance of resistance, making pollution monitoring relevant to the same health issue.

This link explains why antimicrobial resistance is addressed in the One Health approach. The concept starts from the fact that the health of people, animals, and ecosystems cannot be managed separately when the same biological agents and environmental pressures circulate among these domains.

For the EU, One Health represents the framework in which public health, veterinary medicine, agriculture, and environmental protection policies can be coordinated. Wastewater monitoring would allow for the connection of these areas through a common set of data regarding how resistance moves between sources and communities.

The analysis considers the method particularly relevant in regions with insufficient health infrastructure, high levels of antibiotic pollution, and limited access to medical services. It is precisely in these regions, however, that implementation is most difficult, as the lack of centralized sewage networks makes the collection of representative samples much more complicated.

This contradiction may exacerbate global disparities in antimicrobial resistance surveillance. Communities with the highest exposure risk may simultaneously be those for which there is the least data and the lowest technical capacity for monitoring.

The issue also has an environmental justice dimension. Populations without adequate access to sewage and clean water are more exposed to contact with contaminated water that may contain bacteria and resistance genes, and many of the same communities are more vulnerable to flooding, extreme temperatures, and other effects of climate change.

Such events can alter the circulation of microorganisms. Floods can mix wastewater with water sources and inhabited environments, while high temperatures can influence the survival of microorganisms and genetic exchanges, further complicating resistance control.

Transforming wastewater monitoring into an operational system requires more than just periodic sample collection. Genetic analysis must identify resistance genes, priority pathogens, and the genetic diversity present in each sample, and the results must be compared with data from other regions and with medical, agricultural, and environmental information.

An important technical obstacle is establishing the microorganism that harbors a particular resistance gene. Detecting a gene in wastewater does not automatically show which bacterial species carries it or the likelihood that it will cause a human infection, which limits the precision of risk assessment.

Standardization is another issue. Results obtained from two cities cannot be reliably compared if the samples are collected differently, use different sequencing technologies, or are analyzed by incompatible methods.

The author of the study therefore recommends common international standards for sample collection, processing of biological material, genetic sequencing, and data interpretation. A global system would also require long-term investments, as monitoring must be maintained long enough for developments and genetic changes to be observed.

There are also issues regarding data protection. A sample from a large municipal system represents a population large enough that individual identification may be difficult, but samples from very small buildings or communities may contain information that, under certain conditions, allows for the deduction of sensitive data.

The research recommends developing rules regarding confidentiality, consent, data management, and how results are communicated to the public. These standards are necessary to avoid situations where monitoring a hospital, a community, or a region produces stigmatization or allows for the indirect identification of individuals.

Genetic data must also be transformed into usable information for authorities. Detecting thousands of sequences does not automatically produce a public health decision, and the analysis highlights the need for systems that combine environmental data with clinical, agricultural, and pharmaceutical information.

Such a system could allow for the identification of the link between an increase in a particular resistance gene in sewage and changes in antibiotic prescribing, hospital activity, agricultural practices, or pollution from an industrial facility.

Proposed priorities include dedicated funding for monitoring, pilot programs in resource-limited regions, international standards for methodology, and investments in technologies that make genetic analysis more accessible and easier to apply in different sewage infrastructures.

The ultimate goal is for monitoring to function as an early warning system. Identifying a new gene in a region or observing its transfer to other microorganisms could allow for interventions before that particular form of resistance becomes common in human infections.

The analysis does not claim that wastewater monitoring can replace clinical testing, hospital surveillance, or control of antibiotic use. It proposes integrating the method into a broader system, where environmental information complements data from humans and animals.

The results presented by DG Environment come from a perspective article and a literature analysis conducted by researcher José Luis Balcázar. The material does not represent a new policy adopted by the European Commission and does not announce the creation of a mandatory European system for monitoring wastewater for antimicrobial resistance.

The Commission also specifies that the material summarizes a single study and that the opinions and conclusions of the independent research do not necessarily represent the institutional position of the European Commission. Other studies may reach different conclusions.

Antimicrobial resistance reduces the effectiveness of antibiotics and other drugs used against microorganisms and is one of the European priorities in the One Health field. The approach aims to coordinate human and veterinary health with agriculture and ecosystem protection, as the use and spread of antimicrobials cannot be limited to a single sector.

Wastewater monitoring has been significantly expanded during the COVID-19 pandemic, when sewage analysis allowed for the identification of trends in virus circulation at the community level. The current research proposes using the same logic for antibiotic resistance genes, but with more complex genetic and analytical tools.

Integrating such a system into long-term strategies would require international coordination, common standards, and sustained investments. The desired advantage would be the detection of emerging resistance before new genes spread to other microorganisms, regions, and populations and become a clinically difficult problem to control.