Role of Whole Genome Sequencing in the Public Health Surveillance of Foodborne Pathogens

Abstract

Whole genome sequencing shows promise to transform public health microbiology of foodborne pathogens. The technology could replace almost all traditional workflows in a typical public health laboratory with a single cost-efficient whole genome sequencing workflow that includes all organisms. This workflow would include identification and reference characterization, e.g., serotyping, virulence characterization and antimicrobial resistance determination, and high discriminatory subtyping for outbreak detection and investigation. A multi-locus sequence typing (MLST) based analytical approach is the optimal primary subtyping tool for public health because it may be performed by laboratory personnel with little understanding of bioinformatics, be tiered at different level of discrimination for different public health purposes, and all subtypes are stable and may therefore be named definitively. Stable nomenclature is critical for efficient communication between public health partners to follow trends and for outbreak investigations. Unlike MLST, single nucleotide polymorphism based approaches rarely lead to stable nomenclature and should therefore be reserved for situations where MLST does not provide unequivocal answers.