What is the PATH-SAFE Programme?
Last updated
Last updated
PATH-SAFE aims to improve national surveillance of foodborne diseases and antimicrobial resistance through environmental sampling & DNA sequencing. It is an operationally-focused data platform which standardises assembly and analysis of pathogen isolates from several organisations, with a particular focus on foodborne salmonella.
This exemplar National FBD Genomic Data Platform is a cross-government effort aiming to improve the characterisation and tracking of FBD pathogens and AMR, share information, and connect government and public data. The platform (focusing at present on Salmonella) provides genomic analytics to support the identification of clusters of interest, visualised in user-friendly reports. The design and features of this have been derived from extensive end-user research and evidence-building aiming to provide maximum value and impact for users.
This work has been conducted through the Pathogen Surveillance in Agriculture, Food and Environment (PATH-SAFE) research programme which is funded by a Shared Outcomes Fund (SOF) from HM Treasury.
More information can be found on the Food Standards Agency (FSA) site:
Foodborne diseases (FBD) present a significant public health threat, causing 2.4 million individual illnesses and over 16,000 hospitalizations annually. The primary culprits are a few bacteria entering the food chain from farmed animals or the environment. Beyond FBD, the agri-food supply chain is a potential conduit for antimicrobial resistance (AMR) transmission through food, animals, humans, and water. Despite the UK's progress in reducing antibiotic use in humans and animals, drug-resistant bloodstream infections surged by 32% from 2015 to 2019, contributing to the emergence of untreatable 'superbugs.'
To address these challenges, the UK government has leveraged technological and data management advancements to enhance surveillance and safeguard public health. The Pathogen Surveillance in Agriculture, Food and Environment (PATH-SAFE) programme is a £19.2 million Shared Outcomes Fund (SOF) research programme which aims to develop a national surveillance programme for foodborne diseases and antimicrobial resistance.
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
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
provide better data to identify the prevalence, source and pathways of FBD and AMR, helping to prevent spread by enhanced targeting of interventions
4 WorkStreams
WS1: National foodborne disease genomic platform (using Pathogenwatch, the user-facing software underlying the PATH-SAFE platform)
WS2: New Surveillance approaches
WS3: Rapid, in-field diagnostic technologies
WS4: Environmental AMR surveillance system pilot
aggregate WGS data from foodborne isolates from human, food, feed, animal and environmental samples
standardise WGS assembly and analysis to ensure comparability of genomes
enable inter-agency data exchange without compromising data security
enable the detection of joint clusters of human and non-human isolates
stimulate inter-agency investigations
Overview of the data flow in PATH-SAFE:
The basis for the WS1 Data Platform is a combination of Data Storage () and Interactive Analysis (Pathogenwatch, the user-facing software underlying the PATH-SAFE platform).
