Advances in foodborne outbreak investigation and source tracking using whole genome sequencing

The progress in sequencing technology has revolutionized the fields of public health and food microbiology. Today, whole genome sequencing allows high-throughput analysis of entire bacterial genomes at affordable costs. Whole genome sequencing has become a daily routine process for surveillance of foodborne infectious diseases, outbreak investigation, and pathogen source tracking. Several studies on a variety of bacterial species have shown that whole genome sequence-based typing approaches are currently the most powerful typing tools. Whole genome sequencing allows the extraction of information on phylogenetic relatedness, antibiotic resistance, virulence-traits, serotype and multilocus sequence type of an isolate from a single analysis. The optimal typing resolution achievable by whole genome sequencing makes it possible to monitor even small genetic variations occurring in an outbreak strain during the course of an outbreak, making transmission events traceable. Whole genome sequencing allowed the creation of global databases based on standardized nomenclatures like the current multilocus sequence type databases. The benefit of global databases is the international exchange of data as a prerequisite for cross border outbreak investigation, strain tracking, and source identification in the global food chain. With further technological advancement, metagenomic approaches may provide future solutions, allowing complete pathogen detection and characterization directly from specimens.