Next generation sequencing-based multigene panel for high throughput detection of food-borne pathogens

Area of Science:

• Food safety and microbiology
• Molecular diagnostics
• Bioinformatics

Background:

• Foodborne diseases pose a significant public health risk, necessitating accurate and rapid detection of foodborne pathogens (FBPs).
• Current detection methods, often relying on classical cultivation, can be time-consuming and less efficient for identifying multiple pathogens simultaneously.
• There is a continuous demand for advanced analytical methods to ensure the safety of food products.

Purpose of the Study:

• To develop and validate a multiplex PCR-based Illumina sequencing method for the simultaneous detection of multiple FBPs in food matrices.
• To create a specialized primer collection, the foodborne pathogen panel (FPP), for enhanced FBP identification.
• To establish a rapid, sensitive, and specific method for ensuring food safety.

Main Methods:

• Development of a novel primer collection (FPP) comprising 12 oligonucleotide pairs from an initial set of 25 bacterial targets and 49 primer pairs.
• Application of a multiplex PCR-based Illumina sequencing approach for FBP detection.
• Bioinformatics-based identification of detected pathogens.

Main Results:

• The FPP enables the simultaneous identification of eight key bacterial pathogens: Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Salmonella enterica subsp. enterica serovar enteritidis, Escherichia coli, Shigella sonnei, Staphylococcus aureus, and Yersinia enterocolitica.
• The method achieves a sensitive detection threshold of 10^1 cell/g in various food matrices.
• The entire process, from sample acquisition to bioinformatics identification, is completed within approximately two days.

Conclusions:

• The developed FPP multiplex PCR-Illumina sequencing method offers a rapid, reliable, sensitive, and specific alternative or complement to existing PCR techniques for FBP detection.
• This method can be integrated into food quality control systems throughout the food chain.
• It significantly enhances the ability to ensure food safety and minimize the risk of foodborne illnesses.