Is Whole Genome Sequencing Really Replacing Traditional Microbiology?

The genetic sequence of a microorganism carries most of the information that determines its phenotypic characteristics. For that reason, theoretically whole genome sequencing (WGS) could replace almost all traditional workflows in a typical public health laboratory with a single efficient workflow to be used with all foodborne pathogens. This workflow would include identification and reference characterization, e.g., species identification, serotyping, virulence characterization and antimicrobial resistance determination, and high discriminatory subtyping for outbreak detection and investigation.

But is it feasible to make this transformation?

With the introduction of the next-generation sequencing technologies, determining the whole sequence of a foodborne bacterium may be completed in a matter of hours or days at a cost that compares favorably with traditional methods. The Centers for Disease Control & Prevention (CDC) together with partners in the federal food regulatory agencies, the National Center for Biotechnology Information (NCBI), the Association of Public Health Laboratories (APHL) and the states recently completed and proved the utility of WGS for real-time surveillance of listeriosis in United States. PulseNet, the national molecular surveillance network for foodborne infections, is now implementing the technology not just for outbreak surveillance but also for reference characterization of foodborne pathogens. Pilot databases and analytical tools that do not require bioinformatics skills of the end user have been developed and is under validation with partners in the states and abroad for Listeria monocytogenes, Campylobacter and Shiga toxin-producing E. coli (STEC). A pilot database for Salmonella is under construction. WGS is replacing traditional microbiology of foodborne pathogens.