The use of next generation sequencing for improving food safety: Translation into practice

February 27, 2019


Sébastien Leuillet, Chief Technology Officer, Biofortis Mérieux NutriSciences. 


This work was conducted by an expert group brought together by the European branch of the International Life Sciences Institute (ILSI Europe), with support from the ILSI North America Food Microbiology Committee, ILSI Japan Next Generation Sequencing Project, and ILSI Southeast Asia Region. The expert group and this publication were coordinated by the ILSI Europe Microbiological Food Safety Task Force. Biofortis Mérieux NutriSciences is one of the industry members of this task force and co-authored this paper. The complete list of industry members can be found on the ILSI Europe web-site at


Guidance is provided for new users, such as public health departments and the food industry, on the implementation of Next Generation Sequencing (NGS) and how to critically interpret results and place them in a broader context. The review aims to promote the broader application of NGS technologies within the food industry as well as highlight knowledge gaps and novel applications of NGS with the aim of driving future research and increasing food safety outputs from its wider use.

Next Generation Sequencing (NGS) combined with powerful bioinformatic approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of single isolates allows the most detailed comparison possible hitherto of individual strains. The two principle approaches for strain discrimination, single nucleotide polymorphism (SNP) analysis and genomic multi-locus sequence typing (MLST) are showing concordant results for phylogenetic clustering and are complementary to each other. Metabarcoding and metagenomics, applied to total DNA isolated from either food materials or the production environment, allows the identification of complete microbial populations. Metagenomics identifies the entire gene content and when coupled to transcriptomics or proteomics, allows the identification of functional capacity and biochemical activity of microbial populations.



The Highlight of the review are:

  • Advances in sequencing technologies and bioinformatics are ushering in rapid changes in food microbiology.

  • SNP and genomic MLST based WGS analyses for strain discrimination are complementary to each other.

  • In source tracking investigations, WGS results must be backed up by epidemiological and other investigative evidence.

  • Metabarcoding identifies complete microbial populations; metagenomics also determines hypothetical functional repertoire.

  • Harmonisation and standardisation has to be addressed and data sharing incentivised.


A selection of the more commonly used tools as well as bioinformatic suites containing such tools, are provided. The critical issue of Interpretation of results is discussed, as well as 'the need for standardisation', together with the industry implementation considerations. The authors finnally discuss the actual challenges to be addressed.


You can find the free-access to the full text on Science direct


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