Whole Genome Sequencing for Food Safety, Clinical and Public Health Microbiology

Abstract

Whole genome sequencing (WGS) has become the new technological standard in public health surveillance and disease control systems worldwide. WGS allows the most accurate identification and detailed characterization of microorganisms and is a significant improvement in outbreak investigation, source identification, tracking and surveillance, infection prevention and control in public health microbiology. This allows assurance and risk assessment of food microorganisms and microbial risk management. The high data quality, the reproducibility, stability and accuracy of WGS technology has been demonstrated. WGS passed its acid test with flying colors during the COVID-19 pandemic where the technology was successfully used for early detection of new virus variants improving risk assessment and public health measurements. With the ongoing development of the entire WGS system i.e. technology, metadata, new bioinformatics and machine learning algorithms, we can expect a paradigm shift from classical/ molecular microbiology towards precision microbiology.