PATHSAFE data system for the rapid interrogation and archiving of genomic data

Tender description

Background  The Pathogen Surveillance in Agriculture, Food and Environment (PATH-SAFE) programme is a £19.2m Shared Outcomes Fund (SOF) research programme. It aims to develop a national surveillance network, using the latest DNA-sequencing technology and environmental sampling to improve the detection, and tracking of foodborne human pathogens and AMR through the whole agri-food system from farm-to-fork.   The heart of this 'virtual' network will be a new data platform that will permit the analysis, storage and sharing of pathogen sequence and source data, collected from multiple locations across the UK by diverse government and public organisations (incl. FSA, FSS, DHSC, Defra and others across the devolved administrations).  This single, user-friendly data system will enable rapid identification and tracking of foodborne pathogens and AMR, improving public health, and minimising the economic and environmental impact of outbreaks.   By creating a fully integrated surveillance system, we have the potential to not only collect and 'mine' this data in different ways, but also create efficiencies by additionally testing samples collected for one purpose for foodborne pathogens and by having data that can be readily shared between different partners.  Through this pilot project, we will establish a One Health Approach (taking a systems-based view, integrating human, animal, and environmental health), with the establishment of shared technology platforms and common data standards. This approach will directly contribute to the government's 20-year vision and the AMR National Action Plan1, which has made a major, pan-government commitment to countering the risks associated with AMR.  The government has highlighted that the development of new diagnostics and improved access to and use of surveillance data are key levers to tackle this rapid rise and the associated costs of drug-resistant infections through agriculture, food, and the environment. The PATHSAFE programme has 4 core workstreams (WS) as detailed below.  This pre-engagement advert relates to Workstream 1.   'Establish a curated, national foodborne disease genomic data platform '