DirectPred – Same-day pathogen mitigation through direct sequencing and AI

Rapid and reliable identification of foodborne pathogens is essential for food safety management in the dairy and food industry. Today, surveillance is largely based on conventional microbiological methods that require culturing and purification of bacteria. These methods are well established but time-consuming, with results often available only after several days. This limits their use for timely decision-making and provides limited resolution when distinguishing between closely related bacterial strains.

By: Anne Lau Heckmann

The aim of DirectPred is to develop an approach that combines direct DNA sequencing and artificial intelligence to enable identification and characterisation of pathogens within one working day. Building on experience from the earlier LisPred project, DirectPred works directly on enrichment samples and removes the need for purification and colony selection.  When contamination is detected, rapid insight into the characteristics of the detected strain is essential for assessing risk, selecting mitigation measures, and preventing persistence. 

Using long-read sequencing combined with bioinformatics and machine learning, DirectPred will identify bacterial species and predict key characteristics such as sequence type, serotype, virulence potential, and disinfectant resistance directly from enrichment samples. The project consists of four components: direct identification of the bacterial species, bioinformatic interpretation using AI, validation of effectiveness, and development of a standalone tool. DirectPred will be tested and implemented at service laboratories at ISI Foods and Arla Foods HOCO. The final outcome is a freely available, standalone and user-friendly tool that can be implemented in laboratories already performing routine pathogen detection, without requiring specialised expertise in genomics or advanced computing.

By shortening the time from detection to characterisation, DirectPred contributes to improved pathogen control, more precise root-cause analysis, and better-informed risk management. While initially focused on Listeria monocytogenes, the approach can potentially be extended to other foodborne pathogens. By reducing processing time and improving pathogen control, the project contributes, among other things, to enhanced food safety and global competitiveness benefiting both large and small companies.