Role Of Whole Genome Sequencing In Food Safety

Food safety is becoming a public health priority and governments are making efforts to develop policies and regulatory frameworks, establish and implement effective food safety systems to ensure that food producers and suppliers along the entire food chain operate responsibly and supply safe food to consumers.

- Dr. K. V. Satyanarayana

The epidemiological investigation of a food-borne outbreak, which includes identification of pathogen, source attribution, removal of contaminated food items from the supply chain and development of other intervention strategies, depends on the ability to subtype the etiological agent at a high enough resolution to differentiate related from non-related cases. The traditional phenotypic subtyping methods used include serotyping, phage typing and biotyping. Since 1990, the field of subtyping has been revolutionized with the advent of molecular and DNA-based subtyping methods, which allow more sensitive discrimination than the traditional methods. Commonly used molecular subtyping/genotyping methods include banding pattern-based Pulse Field Gel Electrophoresis (PFGE), and DNA sequencing-based Multi Locus Sequence Typing (MLST), and Multiple Locus Variable Number Tandem Repeat Analysis (MLVA). The establishment of PulseNet in USA in 1996 and its expansion as “PulseNet International” was instrumental in advancing the adoption of molecular subtyping for bacterial food-borne disease surveillance. PulseNet selected PFGE as the primary genotyping methodology, which substantially advanced food-borne disease surveillance and outbreak investigation.

Whole genome sequencing (WGS)

Whole genome sequencing (WGS) is a laboratory procedure that determines the complete DNA sequence in the genome of an organism in one process. Recent advances in sequencing technologies and bioinformatics tools have made WGS a viable and advanced solution for epidemiologic investigation and surveillance of food-borne bacterial pathogens. Due to its advantages over PFGE, WGS is now becoming the preferred method for organism identification and comparison among isolates.

Advantages/benefits of WGS