Shellfish as bioindicators for coastal antimicrobial resistance - summary
Published 26 October 2023
Applies to England
© Crown copyright 2023
This publication is licensed under the terms of the Open Government Licence v3.0 except where otherwise stated. To view this licence, visit nationalarchives.gov.uk/doc/open-government-licence/version/3 or write to the Information Policy Team, The National Archives, Kew, London TW9 4DU, or email: psi@nationalarchives.gov.uk.
Where we have identified any third party copyright information you will need to obtain permission from the copyright holders concerned.
This publication is available at https://www.gov.uk/government/publications/shellfish-as-bioindicator-for-coastal-antimicrobial-resistance/shellfish-as-bioindicator-for-coastal-antimicrobial-resistance-summary
1. Chief Scientist’s Group report summary
This pilot research study sought to develop a suite of testing approaches to assess the presence and identity of antimicrobials and resistant microorganisms in marine shellfish. The filter feeding habit of these creatures means they may provide a sentinel species to report on water quality in respect of antimicrobial resistance while minimising costs through using samples already collected for other purposes.
1.1 Background
Antimicrobial resistance represents a major concern for humans, animals, plants and the wider environment. The government’s 5-year National Plan outlines how the UK will address the AMR challenge and includes specific reference to the need for better understanding of the spread, transmission and risk of AMR in the environment. Filter-feeding shellfish present a potentially useful sentinel bioindicator model to help address this current gap in environmental AMR surveillance. Bivalve species are capable of greatly concentrating microbial contamination from the environment and are already examined regularly in Europe for bacterial faecal indicator organisms (Escherichia coli, E. coli) as part of various monitoring programmes.
1.2 Approach
Shellfish waters are currently monitored for a range of substances and the microbiological quality of shellfish flesh. For this work we used some of the bivalve shellfish samples obtained during routine sampling and further tested for AMR. Shellfish taken from five sites in July 2022 to January 2023 were tested using chemical, molecular (AMR gene and metagenomic analysis) and microbiological approaches (E. coli isolation and susceptibility testing).
1.3 Findings and outlook
We developed a set of sample processing and extraction methods that can be used to isolate DNA from a diverse range of live bivalve shellfish species (oysters and mussels). We were then able to use shellfish samples, collected as part of ongoing statutory monitoring programmes and a range of E. coli strains were isolated and tested, generating useful baseline data on the prevalence of resistance genes in these indicator organisms.
A potential seasonal trend was observed at some sites for the presence of AMR genes (e.g., higher abundance of beta-lactamase genes in the summer than autumn these genes enable resistance to penicillin and similar antibiotics) and for trimethoprim (higher levels were detected in samples from November onwards as opposed to summer samples). Further work is needed to confirm the validity of these trends.
We also implemented a targeted mass spectrometric method for a range of antibiotics, antifungals and their metabolites. With this we identified the presence of antibiotics (clarithromycin and trimethoprim) and the antifungal clotrimazole in bivalve shellfish samples. Using High-Resolution Mass Spectrometry (HRMS) Screening provided to be an additional tool in the AMR assessment as it allows screening of samples at lower sensitivity.
This study showed that shellfish can be used as sentinels for monitoring AMR in the coastal environment and given further developmental work have the potential to be used more widely for environmental purposes.
1.4 Publication details
This summary relates to information from project SC220004, reported in detail in the following output:
- Report: SC220004
- Title: Shellfish as bioindicators for coastal antimicrobial resistance
- Project manager: Dr Wiebke Schmidt, Chief Scientist’s Group
This project was undertaken 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. The project was carried out in collaboration with Cefas and was as part of the Environment Agency Chief Scientist’s Group research into AMR in the environment and has been funded by the PATH-SAFE programme which has been funded by HM Treasury through the Shared Outcomes Fund.
Enquiries: research@environment-agency.gov.uk.
© Environment Agency