Research and analysis

Evaluating microbial DNA markers in archived bathing water samples: summary

Published 29 September 2026

Applies to England

1. Chief Scientist’s Group report summary

This project evaluated the use of an emerging methodology to determine levels of microbial DNA markers in bathing water samples. Quantitative polymerase chain reaction (qPCR) can measure highly specific DNA sequences associated with particular organisms. In this research we demonstrated how high throughput qPCR (HT-qPCR) could be used to detect multiple markers in archived bathing water samples from 2023. We also identified how the presence of these markers changes as environmental conditions change. This study does not establish health risk thresholds, which would require complementary epidemiological studies.

1.1 Background

The Environment Agency monitors and classifies microbial water quality at designated bathing waters during the bathing season so the public can make informed decisions. This statutory monitoring relies on culturing two indicator bacteria (E. coli and intestinal Enterococci), used as faecal indicator organisms (FIOs). However, it is widely recognised that these indicators do not reflect all potential waterborne pathogens, some of which do not follow a faecal-oral transmission route or may exhibit antimicrobial resistance.

The Environment Agency routinely freezes a proportion of bathing water samples for potential investigations, whereby conventional qPCR is used to help identify likely sources of pollution should they occur. HT-qPCR could expand on this approach by measuring a range of specified microbial DNA markers as a targeted screening method. Because qPCR measures DNA rather than living organisms, it can detect markers from living and dead organisms, as well as extracellular DNA fragments. Unlike the current FIO method, which only measures living organisms, this broadens the information captured from a single spot sample. However, it also means that detecting microbial DNA markers does not necessarily indicate a health risk. Moreover, certain markers could be undetected as some qPCR assays are less sensitive than others.

1.2 Approach

235 samples from the 2023 bathing season were analysed, covering eleven bathing waters; eight coastal, one estuarine, one river and one lake. For each sample 36 microbial DNA markers were quantified from environmental DNA using HT-qPCR. The subsequent assessment included markers targeting 18 pathogens, as well as markers for microbial source tracking, bacteriophages and resistance genes. Samples were compared with existing FIO measurements as well as information on weather, tides and sewerage discharges to contextualise findings.

1.3 Results

There were distinct differences in microbial DNA markers between sites and samples. Out of the 18 pathogen DNA markers analysed, nine were detected in at least one sample. Markers targeting Enterococcus faecalis and Salmonella enterica serovar Typhi were the most frequently detected (in almost every sample), with markers for Acinetobacter baumannii, Pseudomonas aeruginosa, Legionella spp. and Shigella spp. also found at every bathing site. Microbial marker abundances were higher in samples from coastal bathing waters classified as Poor and Sufficient compared to samples from Good and Excellent bathing waters. By contrast, there was some evidence that Poor inland waters had lower marker levels than other sites despite a higher FIO presence. Overall, few significant correlations were found between FIOs and microbial DNA markers. Unlike the FIOs, the markers were significantly associated with high particulate matter (as shown by reduced sample filtration volumes). However, both microbial DNA markers and FIOs were strongly associated with onshore wind, rainfall, and sewerage discharges.

1.4 Conclusions

This research demonstrates how HT-qPCR could provide a scalable method for detecting microbial DNA markers associated with pathogens and antimicrobial resistance, to complement established FIO monitoring.

To consider the use of this approach operationally for informing investigations or bathing advice, further work is needed to understand the links between marker presence, microorganism viability and specific human health risks. This work provides a basis for understanding what could be readily detected by a high throughput screening method if such links were established.

1.5 Publication details

This summary relates to information from project SC240046, reported in detail in the following output:

• Report: SC240046/R
• Title: Evaluating microbial DNA markers in archived bathing water samples
• Dataset: SC240046/D
• Title: HT-qPCR data on microbial DNA markers in archived bathing water samples
• Science manager: Dr Martin Spurr, Chief Scientist’s Group

This project was delivered by the Environment Agency’s Chief Scientist’s Group, which provides scientific knowledge, tools and techniques to enable us to protect and manage the environment as effectively as possible.

Enquiries: research@environment-agency.gov.uk.

© Environment Agency