Application of advanced genomic tools in food safety rapid diagnostics: challenges and opportunities

Abstract

The increasing adoption of genomics and sequencing-based approaches to detect foodborne pathogens has led to a new direction in food safety diagnostics. Sequencing technologies such as next-generation sequencing are used to confirm the taxonomic hierarchy and revision, describe a novel species, genome construction, prediction of microbial functions, risk assessment, identify the transmission dynamics, and conduct the routine surveillance of foodborne pathogens. Growing implementation of these culture-independent diagnostics tools by several public health, clinical, governmental, and industrial entities to replace the slow and labor-intensive culture-dependent methods underscores the impact of sequencing-based methods. This review focuses on the emerging computational genomics and bioinformatics approaches for rapid detection and characterization of foodborne pathogens to improve the resolution of molecular diagnostics. • Next-generation sequencing tools facilitate rapid detection of foodborne pathogens. • Sequencing-based methods yield results faster than culture-based methods. • Long-read sequencing enables rapid strain-level identification. • Deep metagenomic sequencing reduces the need for pure culture in functional analysis. • Machine-learning models improve functional genomics and risk assessment.