Validation of the MinION sequencing platform for the detection of viruses, bacteria and parasites in food

Funding period: 2020-2023
Lead: Dele Ogunremi
Total GRDI funding: $65,500

There is a need to develop and implement an improved rapid and reliable detection method of microbial hazards in fresh fruits and vegetables because of an increase in the number of foodborne outbreaks associated with the consumption of these food types. Because they are perishable foods, testing protocols need to be rapid if regulatory intervention is to be done in a preventive and precise manner. A significant and far-reaching impact of rapid detection will be fully realized if the protocol is universal and able to detect contaminating viruses, bacteria, and parasites. The CFIA Ottawa Laboratory scientists have developed a protocol that allows the detection of any and all microbial organisms on the surface of lettuce using the MinION sequencing device. The success of the assay depends on rigorous sample preparation, rapid DNA sequencing using the MinION sequencer, and rapid bioinformatics analysis including the use of multiple but complementary algorithms. This project is designed to be a collaborative and comprehensive validation exercise involving food labs and various subject matter experts (i.e., in virology, bacteriology, and parasitology) as well other federal partners in the Health portfolio, namely Health Canada and Public Health Agency of Canada. The validated test will be compared with existing procedures in the Compendium of Analytical Methods, and is expected to be rapid, robust, and reproducible.