ABSTRACT
Food safety is everybody’s concern, and ensuring food safety is becoming increasingly important in the context of changing food habits, popularization of mass catering establishments, and the globalization of the food supply. The consumption of food contaminated by microbial pathogens, toxic chemicals, or radioactive materials leads to foodborne diseases (FBDs). High-throughput DNA sequencing methodology has rapidly evolved and new methods are continually being commercialized. This review highlights the recent DNA sequencing-based rapid detection methods to trace contamination routes, link isolates to outbreaks, and analyze microbial populations in novel ways. The application of these methods in the molecular diagnostics of foodborne pathogens (FBPs) focusing on viruses, bacteria, and fungi along with the advantages, limitations, and future perspectives to improve food safety are discussed. The most important difference between both approaches lies in the difference of target used; i.e., for whole-genome sequencing, the nucleic acids are obtained from a pure culture isolate, and in metagenomics, total nucleic acids are retrieved directly from the microbiota present in the environment under investigation.
