CEFAS23-144 Contract for PATHSAFE Pathogen machine learning

Background: As part of the Pathogen Surveillance in Agriculture, Food and Environment (PATHSAFE) programme, Cefas are conducting pilot surveillance studies for key foodborne disease pathogens. Cefas have collected and analysed weekly river water samples over a time series of 2 x 3 month periods. Additional analyses of these samples and data generated is required to generate a tool for predicting the risk of foodborne disease in river catchments and shellfish harvesting areas.

Requirement: Cefas require specialised services to generate 16S rRNA sequence data from river water samples and the subsequent bioinformatic analyses of 16S rRNA and whole genome sequences via a customised pipeline. A machine-learning method is required to be developed for the rapid analysis and interpretation of 16S data, along with a dashboard and customised web platform for visualisation of 16S and microbial genomic results.

DNA samples will be shipped from the UK to UAB by the Environment Agency at nocost to UAB. Whole genome sequence data will be provided to UAB by Cefas.