Research and analysis

Pilot surveillance of antimicrobial resistance in river catchments in England: summary

Published 24 October 2024

Applies to England

1. Chief Scientist’s Group report summary

This report presents the results of a pilot scale approach to detection, identification and quantification of antimicrobial resistance (AMR) in three selected river catchments in England.

1.1 Background

AMR is a significant global concern for human, animal, plant and environmental health. Whilst the impacts of resistance are mostly felt in healthcare or agricultural settings, the environment can play an important role in the development and transmission of resistance. The UK 5-year National Action Plan (2019-2024) set out a commitment to explore sampling and analysis options for environmental AMR surveillance at pilot scale in river catchments.

1.2 Approach

We selected 3 catchments with different land uses and tested a range of methods to investigate the levels of AMR along the length of each river. This included:

• chemical analysis for 41 antimicrobial substances
• numbers of resistant bacterial and fungal indicator organisms
• antimicrobial susceptibility testing of bacterial and fungal isolates
• presence and prevalence of up to 384 antimicrobial resistance genes
• metagenomic sequencing to provide information on the genes present in the microbial community
• whole genome sequencing of selected bacteria taken from the rivers

1.3 Findings

In total, 311 samples were taken from 31 sites along the Crookhurst Beck, Coquet and part of the Trent rivers, between May 2022 and February 2023. We found a range of resistant microorganisms, resistance genes, and antimicrobial substances. Sample sites in urban settings generally contained greater numbers of resistant organisms than in rural sites. Genomic results also suggested that different resistance genes may be aligned with land use, perhaps due to different sources of AMR such as livestock and wastewater. Each testing method had its own advantages and limitations, so applying more than one method for examining resistance permitted a broader insight and complementary assessment of AMR in our pilot rivers.

1.4 Conclusions

Antimicrobial resistant microorganisms, resistance genes and antimicrobial substances were detected in all three of the rivers and across all sites that were sampled, although the levels detected varied across locations and through time. The pilot showed how a set of different methods could be applied in monitoring of environmental AMR. It was notable that likely human derived AMR dominated in two of the three trial rivers (Trent and Coquet) despite their different land use and population settings. Future environmental surveillance should take into consideration that AMR levels within a stretch of a river may be influenced by multiple upstream sources of differing nature.

1.5 Publication details

This summary relates to information from project SC210023/R, reported in detail in the following output:

• Report: SC210023/R
• Title: Pilot surveillance of antimicrobial resistance in river catchments in England
• Project manager: Dr Wiebke Schmidt, Chief Scientist’s Group

This project is the result of research jointly undertaken by the Environment Agency’s Chief Scientist’s Group, the UK Health Security Agency (UKHSA) and the Quadram Institute Bioscience. The project was carried out as part of the Environment Agency Chief Scientist’s Group research into AMR in the environment and as part of the PATH-SAFE programme and was funded by HM Treasury through the Shared Outcome Fund.

Enquiries: research@environment-agency.gov.uk

© Environment Agency