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Pathogen Surveillance in Agriculture, Food and Environment Programme

A £19.2 million Shared Outcomes Fund (SOF) research programme which aims to develop a national surveillance programme for foodborne diseases and antimicrobial resistance.

Last updated: 1 February 2023
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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)

 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
Programme structure organogram

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 archiving 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 and meteorological data, to create new knowledge. 

Partners include: University of Oxford, University of Warwick

Current status: Discovery is complete. The findings from this work will support the development of the exemplar data system, which will be tailored to meet user needs and support rapid decision-making. A summary of the findings will be shared with programme stakeholders in due course. A consortium approach to the delivery of the data platform will be taken. Contracting with consortium partners is in progress. Delivery is set to begin in February 2023.

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: More samples are being sent for whole genome sequencing (starting Jan 2023). 800 samples from animal hosts (wild deer, cattle, pigs, poultry and sheep) have been sequenced to date. These will form the basis of the analysis for the first report, due in April. Isolation of E. coli from shellfish, wastewater, abattoir animals and selected food samples also continues as planned. Expansion of the range of food sample sources is being considered, as is winter wastewater sampling to allow comparison of summer and winter isolates. A first phylogeny of human sample data (which was contributed by a collaborator) has been produced. A first MLST tree (using a combination of PATH-SAFE data and existing Enterobase data) comparing the diversity of blood stream and UTI human samples against livestock, poultry, deer and canine samples has also been produced. Discussions around access to sequencing data from clinical isolates to allow comparison of E. coli genomes from animal, food and the environment with clinical datasets continue. 

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

  • 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: Following a substantial amount of planning and protocol development the Taw and Torridge pilot site wastewater, river water and shellfish sampling and analysis was successfully initiated in January.  Sampling and analysis have also begun at the North Wales pilot site being led by Bangor University. Furthermore, analysis of UKHSA COVID-19 archived wastewater samples for Norovirus is underway at the Environment Agency and the first batch of Norovirus positive samples have been transferred from EA to Cefas for whole genome sequencing.

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 raw milk samples from dairy herds across Great Britain (GB)
  • AMR in imported animal feed 
  • AMR in imported raw pet food discovery work

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

Current status: Alongside the continuation of raw meat E. coli isolate sequencing, sample collection and analysis has started on two other projects, raw milk in collaboration with the National Milk Laboratories and animal feed (raw ingredients and finished feed) in collaboration with a feed mill.  Sheep abattoir recruitment is ongoing for the sheep survey project (FSA, Defra, VMD and APHA) and piloting of methods has started for the cattle survey project (SRUC).

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: Autosamplers have been installed at five Belfast wastewater treatment plants, sampling initiated and bioarchiving underway.  Analysis protocols and bioinformatic workflows development underway, linking in to other workstreams where appropriate.  Silica Particle-Encapsulated DNA (SPEDs) for modelling of pathogen spread development progressing well.

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:  The horizon scanning literature review (in collaboration with the University of Lincoln) has resulted in 13,000 hits on broad potential technologies and 5,000 hits on a more focused ‘known’ FBD diagnostics technologies.  Hits are being tagged per technology to make the next step, review of full text, more efficient.  Technology readiness level (TRL) definitions have now been developed and are undergoing review ahead of being incorporated in to the TRL framework. Outreach to stakeholders and potential end users has generated over 20 responses to date and will continue using a snowballing approach.

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:  20/30 Labs have been awarded the contract to deliver the laboratory aspects of the discovery phase.  The project was initiated in December 2022 and will initially focus on investigating the use of LAMP for the detection of Salmonella spp, Listeria monocytogenes and Norovirus in wastewater, with a secondary aim of also including adenovirus, astrovirus, rotavirus and sapovirus if possible.

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

Current status: Chemical analysis for phase 1 and 2 of the pilot river sampling work is in the final stages. Microbiological analysis (MIC testing) and molecular analysis (high throughput detection and quantification of Antibiotic Resistance with Resistomap) is progressing. The last phase (phase 3) of river catchment sampling will begin in Jan/Feb 2023.

The following other R&D projects remain ongoing and are progressing:

  • ‘AMR shellfish’ project with Cefas 
  • ‘Bioaerosol’ project with WSP, Cranfield university and University of Exeter 
  • 'Disinfectant' project with University of Exeter, UKCEH and Cardiff University
  • ‘Bathing Waters’ project work undertaken by Atkins and UKCEH
  • Wild flora and fauna project (the final report is expected shortly) 
  • Three projects reviewing and exploring different aspects in relation to minimum selection concentrations for antifungals and antibiotics with University of Exeter and UKCEH

Development of the exemplar Environmental Surveillance System (supported by Deloitte) continues. Wireframe meetings took place in December 2022 and January 2023. The Alpha phase of development is concluding and the Beta phase is expected to start in February 2023. Discovery work for a future AMR One Health Surveillance System will resume in Jan 2023.

Several reports related to this work have been published:
Selection of river catchments for environmental antimicrobial resistance (AMR) surveillance pilot & extension of AMR database  
Determining sampling strategy and assessment options for environmental antimicrobial resistance (AMR) in airborne microorganisms

More information

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

Get in touch

If you would like to get in touch with the PATH-safe team, you can email them at