Development of a universal, culture-independent test for sensitive detection of viable foodborne pathogens

Fresh produce are increasingly associated with foodborne disease outbreaks. Rapid diagnosis and surveillance of fresh produce have been hampered by the lack of adequate methods for high sensitivity detection and pathogen identification. In addition, the viability of the detected microbes is also another bottle neck in food safety. In this study, Ruimin Gao et al. have developed a universal culture-independent diagnostic test (CIDT) procedure to detect various microbes contaminating fresh produce including viruses, bacteria and parasites.

They applied metagenomic next-generation sequencing (mNGS) using both Oxford Nanopore and Ion S5 sequencers. For improved sensitivity, they used whole genome amplification (WGA) approach to globally amplify DNA recovered from all the surface contaminants. Furthermore, the viability of bacterial cells were also demonstrated in the improved CIDT procedure, by the incorporation of Propidium monoazide (PMA) reagent which enters dead cells and covalently binds to DNA.

Currently, the aim is to apply long-read Nanopore adaptive sequencing by selectively sequencing certain DNA molecules, enabling enrichment and depletion to further improve on the sensitivity of detection.

In conclusion, the developed CIDT procedure allowed for an objective approach in identifying pathogens more conveniently, rapidly and accurately than traditional molecular methods. The adaptive sequencing based CIDT assay has the potential to become a single, rapid mobile test for the diagnostics and surveillance of foodborne pathogens."