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Whole Genome Sequencing and its role in Food Safety

05 JUL,2017

NFS Correspondent

Food safety is a global concern as unsafe food containing harmful pathogens or chemical substances causes several diseases ranging from diarrhoea to cancers. In 2010, 600 million foodborne illnesses and 420000 deaths occurred due to 31 global food safety hazards and the global burden of foodborne diseases caused by these 31 hazards was 33 million healthy years of life lost due to illness and death (WHO, 2015).

Unsafe food also negatively impacts the food security of nations and affect the economic development by restricting the exports. Hence, food safety is becoming a public health priority and Governments are making efforts in developing policies and regulatory frameworks, establishing and implementing effective food safety systems to ensure that food producers and suppliers along the entire food chain operate responsibly and supply safe food to consumers.

The epidemiological investigation of a foodborne outbreak, that includes identification of pathogen, source attribution, removal of contaminated food items from 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 nonrelated cases. The traditional phenotypic subtyping methods used include serotyping, phage typing and biotyping.

Since 1990s, the field of subtyping was revolutionized with the advent of molecular and DNA based subtyping methods, which allowed more sensitive discrimination than 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 foodborne disease surveillance. PulseNet selected PFGE as the primary genotyping methodology which substantially advanced foodborne disease surveillance and outbreak investigation.


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 foodborne bacterial pathogens (Deng et al. 2016). Due to advantages over PFGE, WGS is now becoming the preferred method for organism identification and comparison among isolates


(a) Regulators and Public Health Agencies

Whole Genome Sequencing (WGS) has already been used in few countries to subtype common foodborne pathogens wherein the high-resolution WGS subtyping data has enhanced the outbreak detection and facilitated epidemiological investigations. The high specificity and sensitivity of WGS provides greater confidence in regulatory decisions made by authorities on food safety, public health etc.


US FDA is utilizing WGS since 2008 and is coordinating efforts by federal, state, and international public health agencies to sequence pathogens collected from foodborne outbreaks, contaminated food products, and environmental sources and make their genomic sequences publicly available in a database called GenomeTrakr. GenomeTrakr, established by the FDA in late 2012, is the first distributed network of labs to utilize WGS for pathogen identification and can be used to help pinpoint the contamination sources of current and future outbreaks.

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