Antimicrobial resistance (AMR) in waterways presents a critical threat. If commonly used antibiotics are deemed useless, decades of progress in human medicine and agriculture could be undermined.
By 2050, AMR could cause 10 million deaths annually, according to the UN Environment Programme. But AMR is not just a human health issue. It also contributes to a decline in water quality and is exacerbated by water pollution, particularly from sources such as sewage and agricultural runoff. So, it’s a significant environmental concern with far-reaching implications.
Addressing AMR in water is challenging because water systems are complex and can carry many different types of resistant bacteria. The lack of efficient, scalable and globally accessible methods to monitor AMR in water makes it difficult to mitigate this growing threat.
I recently published a review in the Sustainable Microbiology journal that identifies key trends in AMR detection methods and highlights significant gaps.
Rivers, lakes and wastewater systems around the world act as reservoirs and pathways for resistant superbugs and their genes, allowing AMR to spread across ecosystems, affecting wildlife, agriculture and human populations. River water is the most studied source of water samples, making up 42% of AMR-related research studies. Other water sources, including lakes and wastewater, may also play a key role in spreading resistant genes but, without detailed analysis, will remain misunderstood.
Most AMR research comes from three countries: the US (17%), China (10%) and Brazil (9%). This shows where the focus is, but many other regions, especially low-income countries, are not well studied. This is concerning because AMR may be even more serious in these areas, yet data is lacking.
To detect AMR, scientists primarily use two advanced molecular methods: polymerase chain reaction (PCR) (used in 57% of studies) and metagenomics (27%), alongside traditional culture-based methods that involve growing bacteria in a lab.
Culture-based methods are simpler and cheaper than molecular methods but cannot be used onsite. They also can’t detect dead bacteria or hidden resistance genes.
PCR amplifies specific DNA sequences for detection and can be used to identify specific bacteria. Metagenomics is a technique that analyses all of the genetic material from entire microbial communities within a sample, offering a broader perspective.
These advanced methods are better at detecting AMR in rivers, lakes and oceans. They can find both known and new types of resistance, making them more useful for thorough monitoring.
In Brazil, scientists used metagenomics to search for all of the different resistance genes present in waterways in different cities. This technique can detect patterns of resistance that regular tests can’t.
While these methods are time-consuming and complicated (because they need specialised equipment and trained staff) and can be expensive, costing thousands of euros, they could be used more widely if funding is available. This would help track antibiotic resistance around the world, making it easier to find and fight.
One Europe-wide study shows that culture methods failed to find all the resistance genes in contaminated river systems in ten countries, while advanced metagenomic techniques were able to identify them. So, molecular tools are crucial for understanding the true extent of AMR.
My review shows a shift towards molecular techniques as the gold standard for AMR detection. It highlights the inadequacies of traditional culture-based methods and the need for integrated approaches that combine molecular techniques such as PCR (for detecting specific resistance genes) with metagenomics (for broader microbial community analysis).
For example, wastewater monitoring programs could use PCR to quickly identify key resistance genes in hotspots while employing metagenomics to map the diversity of resistant organisms. This would offer a more balanced approach that optimises cost, efficiency, and accessibility.
By mapping global research efforts, I identified underrepresented regions such as sub-Saharan Africa and southeast Asia. I also found that certain water sources were underrepresented, particularly rivers in low-income countries. Without more equitable and comprehensive AMR surveillance, those will not be accounted for.
To make accurate AMR detection more accessible to all, hybrid approaches that combine the comprehensive detection capabilities of molecular methods with the affordability of culture-based methods will be essential.
Governments around the world must prioritise investments in technologies that are not only scientifically robust but also economically viable, particularly for low- and middle-income countries.
New methods such as PCR and metagenomics can help us fight the spread of drug resistance. If we can make these methods cheaper and easier to use it could help us manage wastewater better, improve global tracking of drug resistance and make decisions that protect both people and the environment from superbugs.
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Zina Alfahl does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.
