The whole genome sequencing (WGS): a revolution for the Food industry

November 27, 2018

Jérôme Combrisson, our Next Generation Sequencing Industry (NGSI) Manager Europe was an invited speaker at the China International Food Safety and Quality (CIFSQ), last November 7-8th, in Shanghai. Jérome talked about the Whole Genome Sequencing (WGS).


The title of his talk was: ' Listeria Risk: the Role of Whole Genome Sequencing, South Africa Outbreak Case'.


Since 2017, more than 1,000 cases of listeriosis have been reported in South Africa, resulting in the death of 216 people. The source of this epidemic was identified by the use of Whole Genome Sequencing (WGS).


This high-performance technique represents more precise and definitive approaches for epidemiological monitoring and source attribution in the event of a health crisis.


WGS on clinical isolates from a large subgroup of patients has been implemented. 91% of the strains belonged to Sequence Type 6 of Listeria monocytogenes. This same type strain has also been identified in a widely used ready-to-eat poultry meat product. An ST6 strain was subsequently isolated in the production environment of the incriminated manufacturer. On March 4, 2018, the Ministry of Health was able to confirm this product as the source of the outbreak. The fine genome analyzes by WGS between clinical cases and environmental isolates / agri-food products are indisputable. 


The WGS provides the most comprehensive overview of a bacterial strain. The genome composition can be analyzed by using WGS variant identification techniques such as Single Nucleotide Polymorphisms (SNPs/wgSNP) or whole genome MultiLocus Sequence Typing (wgMLST) to identify the virulome, resistome and antibioresistome. MultiLocus Sequence Typing data provides close-to-ultimate discriminatory power to differentiate isolated bacterial strains. This approach has been also demonstrated to be suitable for bacterial strain genotyping/strain typing. Bacterial WGS holds serious promise for enhancing pathogen diagnostics, as well as industrial, agricultural and environmental strain exploration. A variety of applications including comparative genomics (i.e. differentiations between strains, strain typing) can be evaluated through WGS.


How WGS works?

 WGS has greatly transformed the field of epidemiology and is particularly useful for investigating outbreaks of foodborne diseases. WGS allows differentiation between outbreak and non-outbreak strains of foodborne pathogens by comparing their microbial genomes. It has been confirmed that strain typing foodborne pathogens by WGS gives superior resolution to existing subtyping methods such as pulsed-field gel electrophoresis (PFGE). WGS is now used as a method by the FDA and the CDC in the United States to characterize Salmonella and Listeria monocytogenes food and clinical isolates.Agri-food chains are increasingly interested by these techniques to identify perfectly the contamination source and assess the risks associated with contaminating bacteria. Moreover, they will learn that WGS becomes the new international standard for foodborn strain typing. This concrete example  of South Africa outbreak case shows how food company and health authorities can have technical exchanges to really undoubtedly find the pathogen source.


All food company who deal with pathogen's identification and characterization can be interest by the WGS approach, all quality laboratories also when they need source tracking and source identification and to perform strain typing, all microbiology laboratories who want to switch to old strain typing like PFGE to the cutting edges technology Whole Genome Sequencing of foodborn pathogens.



Looking for more informations on WGS? Feel free to contact us at 


Or go to our website by following this link





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