Making AMR monitoring work in wastewater

Composite samples
Traditional approaches to monitoring antimicrobial resistance (AMR) in wastewater have often relied on culturing bacteria. However, this method only reveals a fraction of the resistance landscape, as many resistance genes exist in bacteria that cannot be cultured under standard laboratory conditions. AMR is fundamentally a genetic issue, meaning that resistance genes are embedded within the broader microbial community and can be present in both culturable and non-culturable organisms, as well as in extracellular DNA.

To capture this broader genetic picture, a representative composite sample of wastewater provides the best opportunity to assess the full spectrum of resistance genes present. This typically involves collecting wastewater over a 24-hour period using automated samplers or centralised sampling stations. The sample is then filtered using fine-pore filters to trap as many bacteria as possible. From there environmental DNA (eDNA) can be extracted, capturing the genetic AMR profile at a more complete microbial community level.

Keeping the entire sampling process cold is essential for preserving the microbial community as it exists in the wastewater at the time of collection. If the raw sample is left at room temperature, bacterial populations can continue to grow or die off, leading to changes in the community composition and skewing the results. To prevent this, composite samplers must have refrigerated storage to keep the wastewater cool during collection. After filtration, the membranes (filters) with the captured bacteria should also be kept chilled. The most sensitive stage is while the bacteria are still in the water, this is when community shifts can happen most rapidly. Once filtered, the bacteria are more stable, but cooling should still be maintained to ensure consistency until DNA extraction.‍

‍Frequency
For resistance monitoring to drive meaningful action, results must be generated frequently enough to detect emerging trends and allow for timely interventions. Once antimicrobial resistance genes are widely established in the environment, they become extremely difficult to eliminate. The best strategy is early detection—spotting concerning patterns before they escalate into larger threats.

Ideally, monitoring would take place on a weekly or biweekly basis to provide high-resolution insights. However, as environmental AMR surveillance is still a developing field, establishing a baseline with at least monthly sampling¹ is a realistic and valuable starting point. The earlier we identify shifts, the better equipped we are to respond. Determining the optimal frequency remains a work in progress, balancing feasibility with urgency.

‍Logistics
Now we come to the most challenging part: the logistics behind making the whole process work. As mentioned earlier, for accurate results samples need to be filtered as soon as possible after collection and kept cold until they arrive at the laboratory for DNA extraction. This involves preparing reliable transportation, using containers that maintain a stable cold chain, and allocating sufficient personnel to ensure timely delivery.

And that is just the beginning.

The analysis itself requires highly specialised molecular technology, which can be inaccessible without dedicated infrastructure and technical expertise. In addition, there are thousands of genes associated with resistance to various antibiotics and antimicrobials. The distribution of these genes can vary significantly depending on geography, antibiotic usage practices, and the local microbial ecosystem. As a result, expertise is essential not only for detection, but also for selecting the most relevant gene targets and rigorous quality controlled procedures.

For organisations with in-house laboratory capabilities, this can be a valuable investment. For others, outsourcing the analysis, interpretation, and presentation of genetic data to a specialised partner can significantly reduce the operational burden on the wastewater treatment plant while ensuring speed, consistency, and scientifically robust outcomes.

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Want to explore how your facility can start monitoring AMR? Our services provide solutions from sampling to analysis and results visualised in the Resistomap Platform.

Contact our team through “www.Resistomap.com/contact” for more information 

¹Cutrupi, F., et al. (2024). Towards monitoring the invisible threat: A global approach for tackling AMR in water resources and environment. Frontiers in Water, 6, Article 1362701. https://www.frontiersin.org/journals/water/articles/10.3389/frwa.2024.1362701/full