Pathogen Surveillance in Agriculture, Food and Environment Programme

The Pathogen Surveillance in Agriculture, Food and Environment (PATH-SAFE) programme uses the latest DNA-sequencing technology and environmental sampling to improve the detection and tracking of foodborne disease (FBD) and antimicrobial resistance (AMR).

PATH-SAFE programme background

Foodborne disease (FBD) is a major public health risk with 2.4 million individual illnesses and more than 16,000 hospitalisations per year. Most human disease is caused by a handful of bacteria which enter the food chain from farmed animals or the environment. In addition to FBD, the agri-food supply chain also poses a risk for the transmission of antimicrobial resistance (AMR) through food, animals, humans, and water.

Whilst the UK has made progress in reducing its use of antibiotics in humans and animals in the last five years, drug-resistant bloodstream infections in humans have increased by 32% from 2015 to 2019. The rise and spread of AMR is creating a new generation of ‘superbugs’ that cannot be treated with existing medicines.

For these reasons, government departments already undertake surveillance activities by analysing samples from food, livestock, and humans. Recent advances in technology and data management offer the opportunity to create a step change in surveillance, to protect public health. The PATH-SAFE programme will establish a new data platform that will allow for the analysis, storage and sharing of pathogen sequence and source data, collected from multiple locations across the UK by government departments and public organisations. This single system will enable rapid identification and tracking of FBD and AMR. This will improve public health and minimise the economic and environmental impact of outbreaks.

Aims of the programme

• to pilot a better national surveillance system for the monitoring and tracking of foodborne disease (FBD) and antimicrobial resistance (AMR) in the environment and agri-food system
• to bring together and build on existing initiatives across the UK and to understand what the end-user needs to improve how they work in this space
• to provide better data to identify the prevalence, source and pathways of FBD and AMR, helping to prevent spread by enhanced targeting of interventions

Benefits of the programme

• the information gathered through this pilot will help us to better identify the sources of FBD and AMR
• we expect this pilot will give users better access to relevant data so they can make more informed, evidence-based decisions
• this data can be used to prevent and predict the spread of FBD and AMR by improved, cost-effective targeting of interventions, providing economic savings both for government and industry
• PATH-SAFE will allow us to better identify and react more quickly to emergent diseases (or diseases of increasing concern) through improved surveillance
• this pilot could reduce the number and cost of FBDs and AMR, lower commercial losses, strengthen UK Science Excellence, and enhance the UK food sector’s reputation

Programme structure

The FSA is the lead organisation for the programme, with several core and delivery partners. As the programme develops our partnerships and collaborations continue to grow.

• Food Standards Scotland (FSS)
• Department of Environment, Food and Rural Affairs (Defra)
• Department of Health and Social Care (DHSC)
• UK Health Security Agency (UKHSA)
• Environment Agency (EA)
• Veterinary Medicines Directorate (VMD)
• Animal and Plant Health Agency (APHA)
• Centre for Environment, Fisheries and Aquaculture Science (Cefas)
• Welsh Government
• Scottish Environment Protection Agency (SEPA)
• Bangor University
• University of Oxford
• Queen’s University Belfast
• Fera
• Public Health Wales
• Agri-Food & Biosciences Institute (afbi)
• Department of Agriculture, Environment and Rural Affairs (DAERA)
• National Milk Laboratories (NML)
• Capita
• Deloitte
• University of Worcester
• Quadram Institute
• University of Warwick
• Scotland's Rural College (SRUC)
• Moredun
• Aecom
• Cranfield University
• Scottish E.Coli Reference Laboratory
• Scottish Salmonella, Shigella and Clostridium difficile reference laboratory (SSSCDRL)
• Digital Epidemiology Services
• Ausvet

The Strategic Project Board sits at the top of the governance structure and provides strategic oversight to the programme.

Sitting outside this Board, as independent groups, are the Scientific Advisory Group and the Data Advisory Group.

The Project Delivery Board, supported by the FSA Project Management Team, has four different workstreams from which information is fed:

• workstream 1: National foodborne disease genomic data platform
• workstream 2: New surveillance approaches
• workstream 3: Rapid, in-field diagnostic technologies
• workstream 4: Environmental AMR surveillance system pilot

Funding source and timeline

PATH-SAFE is funded via the Shared Outcomes Fund (SOF). Spending Round 2019 announced £200 million for the Shared Outcomes Fund to fund pilot projects to test innovative ways of working across the public sector.

The first round of the SOF funded a wide range of projects to be run in 2020-21 and 2022-23 the Spending Review 2020 announced a further £200 million was to be made available for a second round of the Shared Outcomes Fund between 2021-22 and 2023-24.

The programme is in phase 2 of the SOF and will run until March 2024. A more detailed timeline and update on key deliverables is under development and will be added here in due course.

Workstream breakdown

Workstream 1: National foodborne disease genomic data platform

Part A: The UK is recognised global leader in genomic database systems. We will utilise this existing expertise, working with academic colleagues and major ‘big data’ stakeholders, to create a user-friendly platform for the rapid interrogation and contextualisation of genomic data. A key element of the data platform development will be allowing the integration of sample data with other existing data sources, for example, infection data, to create new knowledge.

Partners include: Digital Epidemiology Services, University of Oxford, University of Warwick, University of Birmingham

Current status: In August, the delivery team gave an interim progress presentation to the programme management team which generated useful discussion. Work on the platform continues, with a number of months of development left before testing begins in November/December. A programme-wide platform demonstration is being planned for November, which is envisioned will allow greater opportunity for feedback. Key discussions at present are focussed on data integration to the platform.

Part B: The aim of the PATH-SAFE Scottish pilot is to use whole genome sequencing (WGS) to understand source attribution, infection threat, and the level of AMR of E. coli. Samples will be taken from a range of different reservoirs in Scotland. This includes animal hosts, bathing water, wastewater, soil/plants, food, and humans.

Partners include: FSS, Cefas, SEPA, Moredun, Scotland's Rural College (SRUC), MicrobesNG, Public Health Scotland, Scottish E. coli Reference Laboratory, Scottish Salmonella, Shigella and Clostridium Difficile reference laboratory (SSSCDRL).

Current status: Sampling, sequencing and analysis continues as planned. Key highlights from August include:

Two milestones have been completed:

• All E. coli isolates from animal hosts have been sequenced and the metadata has been obtained.
• The remaining 200 E. coli isolates from winter wastewater have been submitted for WGS and are due to complete by the end of the month. All metadata has been obtained.
•  

Additional food sampling aiming to increase the number of food isolates finished the last week of August, with efforts in September focussed on preparation of positive isolates for WGS.

A decision from an application for use of clinical samples (faecal non-STEC) is awaited.

Workstream 2: New surveillance approaches

Part A: Focusing on Foodborne disease (FBD) in the agri-food environment:

• appraise current surveillance systems by identifying existing environmental data and sampling infrastructure for the detection of FBD pathogens.
• explore whether novel analysis technologies (for example WGS of pathogens from wastewater and shellfish) can improve the accuracy, speed and efficiency of outbreak detection and associated risks.
• use high resolution pilot studies (including wastewater and shellfish sampling) at the river catchment scale to determine the feasibility of scaling up to an improved national surveillance infrastructure.
• some of this work will build on existing networks and infrastructure, such as that already in place for water sampling, including recent UK-wide COVID-19 testing initiatives, as well as new approaches.

Partners include: Cefas, Bangor University, Defra, Arup, Welsh Water, Public Health Wales

Current status: The Taw/Torridge catchment summer sampling period successfully concluded at the end of August. Over 1500 isolates have been obtained from the winter Taw/Torridge sampling period, data analysis is ongoing and 500 have been selected for whole genome sequencing. The first draft of the Ribble Rivers Trust report has been received and is being reviewed. The wastewater pilots continue to make good progress; sequencing nearing completion for the Norovirus quantification in UKHSA COVID-19 archived wastewater samples project and sequencing library preparation underway for the Salmonella in Scottish wastewater project. Irrigation water desk study completed and report provided.

Part B: Focusing on antimicrobial resistance (AMR) surveillance in the agri-food environment, a number of projects will support this work:

• Characterisation of AMR E. Coli from raw meat to identify resistance genes and circulating plasmids.
• AMR surveillance sheep abattoir survey, including abattoirs AMR wastewater surveillance pilot.
• AMR surveillance in cattle abattoir survey.
• AMR targets in bulk milk samples from dairy herds across Great Britain (GB).
• AMR in imported animal feed.
• AMR in imported raw pet food discovery work (scoping).

Partners include: VMD, APHA, Cefas, National Milk Laboratories (NML), FSA, Welsh Government, AFBI, Scotland's Rural College (SRUC).

Current status:

Within the raw meat E. coli isolates project, reviews and checks are being undertaken to ensure comparability of results for isolates from 2013 right through to 2022. Sample collection continues to progress as planned for the sheep survey, cattle survey, bulk milk project and animal feed project (raw ingredients and finished feed) with bacteriology results continuing to follow expected trends.

The next PATH-SAFE webinar on 25 September, 2pm to 3pm, will focus on the bulk milk and animal feed projects, including the perspectives of the industry partners whose involvement has made this work possible. Further details and the link to join the webinar.

Part C: Utilise the infrastructure developed for NI SARS-CoV-2 wastewater surveillance programme and undertake building level wastewater monitoring to investigate prevalence of a foodborne disease, norovirus, and antimicrobial resistance within the NI care home setting.

Partners include: DAERA, Queen’s University Belfast, Department of Health (Northern Ireland), Public Health Agency (Northern Ireland), Northern Ireland Environment Agency, Department for Infrastructure (Northern Ireland), Northern Ireland Water.

Current status: Following the receipt of ethics approval, recruitment of nursing homes is underway. Nursing homes that meet the inclusion criteria are currently being canvassed and sewage systems being assessed. Norovirus data from historical wastewater samples is being analysed, including data normalisation and the fitting of regression models. Screening of near-source control site wastewater samples ongoing, including validation of a stabilising agent to improve detection of viral targets in near source wastewater samples.

Part D: This project will utilise existing sample sets and data to investigate source and transmission dynamics of food borne disease (FBD) caused by Campylobacter, including investigation of the spread of antimicrobial resistance (AMR) through Agri-Food systems.

Partners include: University of Oxford, Quadrum Institute

Current status:

Data has been received for a further 384 human disease isolates (making the total 768 so far) from sequencing partner, the Quadrum Institute. These are currently being assembled.

Groundwork for enabling AMR prediction for Campylobacter genomic data on PubMLST is underway. Literature searches to incorporate the latest AMR determinants for Campylobacter and to establish the level of confidence by which AMR determinants can predict phenotype will be completed. Learnings from Klebsiella and Neisseria species will be applied.

Part E: Whole Genome Sequencing of historical Salmonella isolates, to generate background data on the genomic diversity of foodborne pathogens in the UK.

Partners include: AFBI

Current status: Project Complete 31/03/2023 – during February and March 2023 AFBI successfully processed 100 historical salmonella isolates (culture, extraction and sequencing), and uploaded the sequences to Enterobase. PATH-SAFE has been noted in comment field on uploaded sequences in Enterobase to allow identification.

Workstream 3: Rapid, in-field diagnostic technologies

Part A: Investigate the technology readiness levels (TRLs) of in-field FBD and AMR diagnostic technologies. This includes horizon scanning, stage of development and end-user needs. The results of these investigations will inform options for the next stages of in-field testing. The co-design of applications with end-users will be critical to ensure real-world applicability.

Partners include: Fera, University of Lincoln

Current status: Following the selection of 2 ‘in-field’ scenarios and technologies that will be tested in the next stage of the project, connections have been established with the teams working in the selected scenarios. Plans for the testing have been developed and finalised, incorporating: technology verification in the lab, Fera visits to ‘in-field’ locations, end user visit to Fera for training and finally ‘in-field’ testing sessions that will be run in parallel with gold standard methods.

Part B: The key aim of this activity is to repurpose rapid, in-field wastewater diagnostic technology that was developed in response to the COVID-19 pandemic for detection of FBD. This workstream will aim to demonstrate its viability, economic value, and versatility in one or more agri-food settings.

Partners include: UKHSA

Current status: Project Complete 31/03/2023 - 20/30 Labs completed the proof of concept and optimisation work on utilising LAMP on 7 target pathogen - Salmonella spp, Listeria monocytogenes, Norovirus, adenovirus, astrovirus, rotavirus and sapovirus. The final report is undergoing the last stages of review and will be made available in due course.

Workstream 4: Environment AMR surveillance system pilot

The overall aim of this workstream is to create a scientific and evidence-based understanding of the nature and extent of AMR in the environment and the drivers that influence this. This pilot will deliver an agreed and tested methodology for environmental AMR surveillance. This will include an environmental IT platform that will enable a scaled-up surveillance programme to be undertaken. This IT platform will be designed and developed so that it will have the capability to integrate AMR surveillance data collected from humans and animals. The overall ambition is to establish a UK One Health surveillance system for AMR.

Partners include: EA, VMD, Defra, UKHSA, Deloitte, Quadram Institute, Aecom, Cranfield University, University of Exeter, UK Centre for Ecology and Hydrology, Ausvet.

Current status: One R&D project which experienced delays in getting started due to issues with procurement remains in progress. This project is expected to complete by the end of the year. Otherwise, Workstream 4 is considered complete. Final reports are in preparation and workstream closure is in progress.

PATH-SAFE webinar series

PATH-SAFE has started a series of webinar events which will be continuing now until the end of the programme (March 2024). The webinars will showcase results from the programme, as well as invited speakers to discuss topics relevant to programme partners. If you have not already received an invite but would like to attend, please contact pathsafe@food.gov.uk.

Please see below for details of past and upcoming events and links to recordings and presentations we are able to share.

Calendar of webinar events

Please see below for details of upcoming webinars:

Monday 25 September 14:00 - 15:00 - AMR Surveillance Pilots: Dairy Cattle and Animal Feed

During the webinar you will hear from:

• The Animal and Plant Health Authority (APHA) teams who developed the pilot projects and are coordinating and conducting the analysis aspects.
• National Milk Laboratories (NML) and Agricultural Industries Confederation (AIC) representatives talking about who they are, what their organisations do and their perspective of being involved in the PATH-SAFE projects.

Join the meeting on 25 September.

Tuesday 17 October 13:00 - 14:00 - PATH-SAFE Process Evaluation

During the webinar you will hear from RAND Europe who have been commissioned to evaluate the programme:

• to assess the effectiveness and appropriateness of processes underpinning the delivery of the four workstreams (WSs)
• to identify areas for learning and improvement, and to identify how and what PATH-SAFE has contributed to improving surveillance infrastructure

An interim evaluation focussed on processes and identifying areas of improvement has just been completed and the findings will be shared for further reflection to support process improvements moving forward.

Join the meeting on 17 October.

Past webinars and resources

15 March 2023 - "Understanding source attribution, infection threat and level of AMR of E. coli in Scotland using whole genome sequencing”. Dr Adriana Vallejo-Trujillo (Research Fellow, Food Standards Scotland).

Please note the following resources are not accessible. If you require an accessible alternative please contact fsa.communications@food.gov.uk.

Slides from the 15 March 2023 meeting

PDF

View PATH-SAFE FSS Scottish Pilot - ws1b slides as PDF(Open in a new window) (3.53 MB)

Recording of the 15 March 2023 meeting

27 April 2023 - Genomic epidemiology of foodborne pathogens and antimicrobial resistance - A talk from Professor Alison Mather

Unfortunately, due to the sensitivity of content, we are unable to share a recording or slides.

18 May 2023 - PATH-SAFE and The Food Safety Research Network Showcase

Please note the following resources are not accessible. If you require an accessible alternative, please contact fsa.communications@food.gov.uk.

Slides from the 18 May 2023 meeting

PDF

View PATH-SAFE and The Food Safety Research Network Showcase as PDF(Open in a new window) (12.19 MB)

Recording of the 18 May 2023 meeting

Please note due to a technical issue it was not possible to record this webinar.

15 June 2023 - Rapid diagnostic technologies for Foodborne Pathogens

Please note the following resources are not accessible. If you require an accessible alternative, please contact fsa.communications@food.gov.uk.

Slides from the 15 June 2023 meeting

PDF

View Rapid diagnostic technologies for Foodborne Pathogens as PDF(Open in a new window) (873.37 KB)

Recording of the 15 June 2023 meeting

13 July 2023 - 'First steps towards an environmental surveillance system for Antimicrobial Resistance (AMR) in England’

Unfortunately, due to the sensitivity of content, we are unable to share a recording or slides.

Outputs and publications

Below are links to outputs and publications following programme activities. This section will be regularly updated as new publications become available.

WS4 - Scoping review into environmental selection for antifungal resistance and testing methodology. Published on 22 July 2022. This reviews the current understanding of the mechanism for selection for antifungal resistance in fungal species following exposure to antifungals.

WS4 - Antimicrobial resistance surveillance pilot site selection and database extension. Published on 22 July 2022. This project developed selection criteria to identify suitable river catchments for piloting a surveillance programme for environmental antimicrobial resistance.

WS4 - Sampling strategy and assessment options for environmental antimicrobial resistance in airborne microorganisms. Published on 22 July 2022. Reviews the available sampling options for antimicrobial resistant microorganisms, including their antimicrobial resistance genes, from the atmosphere.

WS4 - Antifungal medicines in the terrestrial environment: Levels in biosolids from England and Wales. Published 02 February 2023. Clinical antifungals found in biosolids at treatment centres in England and Wales. Over-the-counter items including ketoconazole and miconazole were most prevalent. Substances introduced at levels that may induce selection pressure for resistance.

WS4 - Environmental surveillance of AMR, perspectives. Published 30 March 2023. A perspective paper on AMR environmental surveillance.

PATH-SAFE Evaluation Framework report. Published 31 July 2023. This report sets out the evaluation framework that will be used to guide the evaluation of the Pathogen Surveillance in Agriculture, Food and Environment (PATH-SAFE) programme.

More information

For more information and updates on the PATH-SAFE programme, read the latest PATH-SAFE newsletter.

PATH-safe newsletter September 2023

PATH-safe newsletter June 2023

PATH safe newsletter March 2023

PDF

View PATH-SAFE newsletter, January 2023 as PDF(Open in a new window) (273.2 KB)

Get in touch

If you would like to get in touch with the PATH-safe team, you can email them at pathsafe@food.gov.uk