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Overview

The work within this theme has focused on three key areas:Ìý

• development of novel surveillance methodologies, approaches and tools
• generation of data on the genomic diversity of a range of foodborne pathogens, and associated antimicrobial resistance (AMR), across the four nations of the UK to establish baselines and address knowledge gaps
• exploration of whole genome sequence data to investigate foodborne pathogen and antimicrobial resistance transmission routes

Collaborating with a range of delivery partners and drawing on their strength and expertise has enabled the delivery of a large portfolio of projects, which have incorporated perspectives and input from across the agri-food system.

Food Standards Scotland (FSS)Ìýhave sequenced thousands of Escherichia coli (E.coli) isolates from a diverse range of sources across Scotland. This will help elucidate transmission dynamics through the agri-food chain and develop machine learning source attribution models for predicting the source or host of origin for E.coli isolates. The team are now sequencing further agri-food related isolates to verify the application of the E. coli source attribution models, looking to demonstrate proof of concept for use of the model in the investigation of foodborne illness and risk management, and extend the approach to develop a similar model for Salmonella Typhimurium (STm).Ìý

The Animal and Plant Health Agency (APHA)Ìý²¹²Ô»åÌýVeterinary Medicines Directorate (VMD), have generated new data and knowledge on antimicrobial resistance (AMR) presence, diversity, and transmission by applying genomics to existing surveillance sampling and initiating novel sampling in understudied compartments of the agri-food chain, particularly ruminants (via bulk milk, and cattle and sheep at slaughter) and animal feed. Whole genome sequence data produced by these projects is now undergoing enhanced genomic analysis to enhance understanding ofÌýAMRÌýdynamics, transmission pathways and mobile genetic elements dissemination. Further novel sampling is being conducted to determine the prevalence ofÌýAMRÌýbacteria in imported raw pet food, and to explore the application of novel abattoir environment sampling approaches as a potential alternative surveillance method that could act as a proxy for existing labour-intensive livestock sampling methods.

The Environment Agency (EA)Ìýhave developed a pilot environmental surveillance system forÌýAMRÌýin the environment, including river water and bathing waters, wild flora and fauna, shellfish and bioaerosols. This work is continuing as part of the Environment Agency research portfolio.Ìý

The Centre for Environment, Fisheries and Aquaculture Science (Cefas)Ìýundertook a river catchment pilot to compare wastewater, river water and shellfish for monitoring of a range of foodborne pathogens, and have worked with the UK Health Security Agency (UKHSA) and the Public Analyst laboratories in Scotland to demonstrate the utility of wastewater for monitoring norovirus and salmonella on a national scale. The team is now continuing the application and advancements of methodologies developed inÌýPATH-SAFEÌýto demonstrate the utility of bivalve molluscan shellfish (BMS), a species routinely sampled through pre-existing surveillance frameworks, as a sentinel in a ‘sample once test many’ approach.ÌýÌý

Bangor UniversityÌýare examining the flow, dynamics and risk posed byÌýAMRÌýand foodborne pathogens (FBP) in wastewater discharges, particularly those originating from healthcare settings. Further work is ongoing to investigate seasonal patterns and potential wastewater treatment opportunities and barriers.Ìý

Food Standards Agency (FSA), UK Health Security Agency (UKHSA), NHS Lothian and CefasÌýare undertaking a project to generate foodborne disease (FBD) prevalence and WGS data from business-as-usualÌýUKHSAÌýpolio wastewater monitoring, utilising methodologies developed by Cefas within theirÌýPATH-SAFEÌýproject. This data will subsequently be compared to data from clinical samples collected throughÌý, presenting an exciting opportunity to align two large surveillance efforts to generate insights into the effectiveness of wastewater monitoring forÌýFBP.ÌýÌý

Queen’s University Belfast (QUB)Ìýhave been investigating the application of air and near-source wastewater monitoring forÌýAMRÌý²¹²Ô»åÌýFBPÌýin a care home setting in Northern Ireland. This work is continuing to explore seasonal trends, increase understanding ofÌýAMRÌýand foodborne pathogens prevalence and transmission, and further evidence the utility of the novel surveillance methods.Ìý

University of OxfordÌýhave sequenced thousands of Campylobacter isolates from a diverse range of collaborators, to help elucidate source attribution and transmission dynamics through the agri-food chain and the rise inÌýAMR. Sequencing and analysis of further human and agri-food Campylobacter isolates is ongoing to determine levels ofÌýAMRÌýin Campylobacter isolates currently circulating in the UK, and enhance understanding ofÌýAMRÌýgene transmission.Ìý

Agri-food and Biosciences Institute (AFBI)Ìýin Northern Ireland selected and sequenced archived isolates of Salmonella and Listeria monocytogenes from food and animal sources, to provide important historical context against which future outbreak sequences can be compared.Ìý

Delivery partners

In addition to the lead delivery partners highlighted in the overview section, a number of other collaborators have supported the delivery of these projects, including:Ìý

• Scottish Environment Protection Agency
• Public Health Scotland
• Scotland’s Rural College
• Moredun Research Institute
• The University of Edinburgh
• Northern Ireland Environment Agency
• Department of Health (NI)
• Agriculture, Environment and Rural Affairs (NI)
• Department of Infrastructure (NI)
• HSC Public Health Agency
• Northern Ireland Water
• Welsh Government
• Public Health Wales
• Welsh Water
• Cardiff University
• South West Water
• Ribble Rivers Trust
• Biosphere North Devon
• Virosafety
• Resistomap
• Quadram Institute
• University of Exeter
• Cranfield University
• UK Pet Food
• Agricultural Industries Confederation
• National Milk Laboratories
• Arla
• UK Centre for Ecology and Hydrology
• Aecom
• Arup
• Capita
• Deloitte
• MicrobesNG

Key successes

Across the theme:Ìý

• more than 8,300Ìýsamples have been collected, across a range of sample sources and four nations
• additional analysis has been undertaken on over 2,500 samples collected as part of existing surveillance activities
• exploration of more than 10,000 archived samples andÌýpathogen isolates
• more thanÌý18,000 pathogen isolates have been sequenced
• increased understanding of methods suitable for environmental monitoring across a range of different media, and development of a pilot environmental surveillance system

Novel surveillance methods, approaches and tools developed and tested using real world samples and data for the first time, including:ÌýÌý

• protocols for isolation and testing of foodborne pathogens from river water, wastewater and shellfish
• ·É²¹²õ³Ù±ð·É²¹³Ù±ð°ù-²ú²¹²õ±ð»åÌýAMRÌý²¹²Ô»åÌýFBDÌý²õ³Ü°ù±¹±ð¾±±ô±ô²¹²Ô³¦±ð sample collection schedules, sample analysis and data analysis pipelines
• machine learning models to determine source/host attribution of pathogens

Contamination and transmission models:

• demonstrable benefit of wastewater-based surveillance, inspiring nursing homes in Northern Ireland to consider wastewater systems design in future builds andÌýsupport wastewater-based surveillance
• large sample volume, broad scope and high throughput nature ofÌýPATH-SAFEÌýprojects have accelerated development and refinement of existing and established methods, including long read sequencing methodologies used byÌýAPHAÌýfor routineÌýAMRÌý²õ³Ü°ù±¹±ð¾±±ô±ô²¹²Ô³¦±ð
• utility of routine whole genome sequencing demonstrated through patterns, trends and insight gained across the programme, including the identification of resistant bacterial isolates of concern within the isolates sequenced forÌýPATH-SAFEÌý
• strengthened cross-government and academia collaborative approach to identifying and pursuing surveillance opportunities, methods development and results analysis
• industry actively involved in the design and conduct of government surveillance activities and promoting theirÌýbenefits, including milk producers and an animal feed mill, in collaboration with National Milk Record and The Agricultural Industries Confederation respectively

Outputs

All projects were presented at theÌýPATH-SAFEÌýBiosurveillance Conference on 28 and 29 February 2024 in London. . 

Summary articles

:ÌýPublished 24 October 2024 on °Ç¸ç³Ô¹Ï, a piece within the Environment Agency’sÌý.

: Published 18 November 2024 in The Microbiologist, Applied Microbiology International’s digital magazine. This piece highlights how evidence generated withinÌýPATH-SAFEÌýhas progressed the understanding ofÌýAMRÌýprevalence and transmission, and illustrates the significant benefits that well-funded, coordinated, cross-sectoral initiatives can deliver.

Environment Agency publications

Scoping review into environmental selection for antifungal resistance and testing methodology:ÌýPublished on 22 July 2022 on °Ç¸ç³Ô¹Ï, this report reviews the current understanding of the mechanism for selection for antifungal resistance in fungal species following exposure to antifungals.Ìý

Antimicrobial resistance surveillance pilot site selection and database extension: Published 22 July 2022 on °Ç¸ç³Ô¹Ï, this project developed selection criteria to identify suitable river catchments for piloting a surveillance programme for environmental antimicrobial resistance.

Sampling strategy and assessment options for environmental antimicrobial resistance in airborne microorganisms:ÌýPublished on 22 July 2022 on °Ç¸ç³Ô¹Ï, this report reviews the available sampling options for antimicrobial resistant microorganisms, including their antimicrobial resistance genes, from the atmosphere.Ìý

:ÌýPublished 2 February 2023 in Science of The Total Environment, this article reports on biosolids from ten sites in England and one in Wales that were sampled and analysed for clinical antifungals.Ìý

:ÌýPublished 30 March 2023 in Eurosurveillance, this is a perspectiveÌýpaper discussing some of the issues and choices that arise inÌýselecting the most appropriate methods for surveillance forÌýAMRÌýinÌýthe environment from the perspective of a government agencyÌýthatÌýconducts routine environmental monitoring for other health-relatedÌýpurposes.Ìý

Environmental antimicrobial resistance: A review of biological methods:ÌýPublished 26 October 2023 on °Ç¸ç³Ô¹Ï, this report reviews biological methods for the detection of environmental antimicrobial resistance.Ìý

Antimicrobial resistance surveillance strategies within wild flora and fauna of England:ÌýPublished 26 October 2023 on °Ç¸ç³Ô¹Ï, this report reviews potential antimicrobial resistance surveillance strategies for wild flora and fauna.Ìý

Shellfish as bioindicator for coastal antimicrobial resistance:ÌýPublished 26 October 2023 on °Ç¸ç³Ô¹Ï, this report covers development of testing approaches to assess the presence and identity of antimicrobials and resistant microorganisms in marine shellfish.Ìý

A review of approaches to monitoring and surveillance of antimicrobial resistance in bathing waters:ÌýPublished 26 October 2023 on °Ç¸ç³Ô¹Ï, this report improves understanding of antimicrobial resistance in relation to human exposures via bathing waters.Ìý

Antimicrobial resistance in bioaerosols: towards a national surveillance strategy:ÌýPublished 26 October 2023 on °Ç¸ç³Ô¹Ï, this report considers the decisions that must be made in designing a national surveillance strategy for antimicrobial resistance in bioaerosols.Ìý

Pilot surveillance of antimicrobial resistance in river catchments in England: Published 24 October 2024 on °Ç¸ç³Ô¹Ï, a pilot approach to detection, identification and quantification of antimicrobial resistance in three selected river catchments in England.

Development of experimental approaches for determining concentrations of antifungals that select for resistance:ÌýPublished 24 October 2024 on °Ç¸ç³Ô¹Ï, methods for the determination of the lowest concentration of antifungals that can lead to a selective advantage for resistant organisms.

Determining selective concentrations for antibiotics and antifungals in natural environments:ÌýPublished 24 October 2024 on °Ç¸ç³Ô¹Ï, this project determined the concentrations of specified antimicrobials at which selection for resistance may occur.

Determining concentrations of substances that influence development of antimicrobial resistance:ÌýPublished 24th October 2024 on °Ç¸ç³Ô¹Ï, this report reviews the available data on concentrations at which selection for antimicrobial resistance has been reported for different antimicrobials and the approaches used to determine these concentrations. This work was also published as a peer-reviewed paper:ÌýPublished 20 August 2024 in Water Research.

Potential impact of disinfectants on antimicrobial resistance development:ÌýPublished 24 October 2024 on °Ç¸ç³Ô¹Ï, this report identifies the range of disinfectants currently used in the UK and reviewed available information on their potential role in the development of antimicrobial resistance.

Risk screening and prioritisation tool for antimicrobial resistance in the environment.Published 24 October 2024 on °Ç¸ç³Ô¹Ï, a risk screening and prioritisation tool to assess antimicrobial resistance in the environment.

Cefas publications

:ÌýPublished November 2023 this article covers development of a duplex RT-qPCR assay thatÌýin wastewater-derived RNA eluents, in a time and cost-effective way and may be used for surveillance to monitor public and .

:ÌýPublished 27 March 2024 on bioRxiv, this article covers the development and optimisation of a long amplicon nanopore-based method for dual-typing the RNA-dependent RNA polymerase (RdRp) and major structural protein (VP1) regions of norovirus, with wastewater as the sample matrix.Ìý

:ÌýPublished 22 June 2024 in Nature Communications, this article presents case studies centred around the recent global approach to tackle antimicrobial resistance and the current interest in wastewater testing, with the concept of ‘one sample many analyses’ to be further explored as the most appropriate means of initiating this endeavour.Ìý

:ÌýPublished 12 September 2024 in Eurosurveillance, this meeting report details to presentations, group discussions, conclusion and recommendations of a workshops hosted byÌýCentre for Environment, Food and Aquaculture Science (Cefas) and Bangor University at the Royal Institution, London, on 31 January 2024.

:ÌýPublished 1 October 2024 in Water Research, this study took approximately 3,200 samples of wastewater from across England, previously collected for quantification of SARS-CoV-2, and re-analysed them for the quantification of norovirus genogroup I (GI) and II (GII). Comparisons of national average norovirus concentrations in wastewater against concomitant norovirus reported case numbers showed a significant linear relationship. Ìý

:ÌýPublished 22 January 2025, this study investigated how different viral concentration methods affect the quantification and long amplicon nanopore sequencing performance for SARS CoV 2 and noroviruses in wastewater.

:ÌýPublished 12 August 2025, this study investigated the challenges and limitations of using monitoring data in catchment‑based models to assess and predict microbiological contamination in river systems.

VMD publications

Ìý(PDF):ÌýPublished 19 November 2024 on °Ç¸ç³Ô¹Ï,Ìýreports the results fromÌýAMRÌý²õ³Ü°ù±¹±ð¾±±ô±ô²¹²Ô³¦±ð pilots in dairy cattle, beef cattle and sheep.

Bangor University publications

:ÌýPublished 10 January 2025 inÌýScience of The Total Environment, this article cover the results from a year-long study, collecting and analysing effluent from three large hospitals, and treated and untreated wastewater from three associated community waste water treatment plants.

:ÌýPublished 22 March 2025 in Environmental Pollution, this article covers the regional-based study that quantified antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacteria in hospital and community-derived wastewater and receiving environments, using high-throughput qPCR (HT-qPCR).

Published 4 September 2025, this study investigated how hydrodynamic modelling can predict the dispersal and fate of norovirus and antimicrobial‑resistance genes in coastal waters originating from community and hospital wastewater sources.

:ÌýPublished 17 May 2025, this study investigated antibiotic resistance genes and human pathogens in hospital wastewater across Wales using metagenomic analysis.Ìý

:ÌýPublished 23 September 2025, this study this study investigated antibiotic‑resistance gene carriers in hospital and municipal wastewater using genome‑resolved metagenomics to reveal how treatment processes shape resistant microbial communities.

APHAÌýpublications

:ÌýPublished 30 January 2024, this study investigated the critical aspects of Antimicrobial Resistance (AMR)ÌýAMRÌýand the dynamics ofÌýAMRÌýin poultry in the UK.

:ÌýPublished 6 October 2025, this study provides an improved understanding of the prevalence, distribution, and subtypes of Salmonella present in slaughter sheep.

Queen’s University Belfast publications

:ÌýPublished 24 June 2025, this scoping review maps the extent of available literature on Wastewater-based epidemiology studies addressingÌýAMRÌýin care homes for older adults.

AFBI publications

:ÌýÌýPublished 3 December 2025, This report summarises the work undertaken by the Pathogen Genomics Unit, Bacteriology Branch, of the Agri-Food & Biosciences Institute, as part of theÌýPATH-SAFEÌýProgramme.

Methodology publications

Cefas:Ìý.

Data

FSS:Ìý(locate sequencing by searching the ‘Comment’ field for ‘PATH-SAFE’ and ‘PATH-SAFEÌýproject’.

Cefas:Ìý.

Cefas:Ìý.

University of Oxford:Ìý.

AFBI:Ìý.

AFBI:Ìý(locate sequencing by searching the ‘Comment’ field for ‘PATH-SAFE’ and ‘PATH-SAFE_23_24’).

Bangor University:Ìý