Same-day multiplex detection of foodborne bacterial pathogens for clinical diagnostics and food safety

Abstract Aims This study aims to develop and evaluate a rapid and high-multiplex pathogen detection method for clinical and food specimens to address the ongoing public health threat of foodborne infections and the limitations of conventional culture-based diagnostics. Methods and results The foodborne bacteria (FBB) assay integrates multiplex PCR, T7 exonuclease hydrolysis, and a suspension bead array to simultaneously detect 16 genes from 13 major foodborne bacteria. Analytical performance was evaluated using reference strains, while diagnostic performance was assessed using clinical and food samples. The FBB assay demonstrated high specificity and sensitivity, with minimum detectable amounts ranging from 5 to 100 copies per reaction for all targets except one. Among 106 clinical specimens from foodborne outbreaks, the assay achieved 99.1–100% overall % agreement with routine methods. In spiked food samples, Bacillus cereus was detected at 1 CFU g-1 in cooked rice, and Listeria monocytogenes at 10² CFU mL-1 in milk; for the latter, sensitivity improved to 10 CFU mL-1 and 1 CFU mL-1 after four and 16 hours of pre-enrichment, respectively. Conclusions The FBB assay enables culture-independent, multiplex detection of foodborne bacterial pathogens within six hours and demonstrates robust analytical and diagnostic performance.