What is the PATH-SAFE Programme?

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.

Pathogen Surveillance in Agriculture, Food and Environment (PATH-SAFE) Programme

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: https://www.food.gov.uk/our-work/pathogen-surveillance-in-agriculture-food-and-environment-path-safe-programme#path-safe-programme-background

Background

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.

The PATH-SAFE programme aims 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

• 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

Programme Structure

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

The WS1 Data Platform Development project aims to

• 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

The basis for the WS1 Data Platform is a combination of Data Storage (CLIMB Big Data) and Interactive Analysis (Pathogenwatch, the user-facing software underlying the PATH-SAFE platform).

Overview of the data flow in PATH-SAFE: