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Food Microbiol. 2019 Jun;79:96-115. doi: 10.1016/ Epub 2018 Nov 17.

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

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Nestlé Research, Nestec Ltd, Route du Jorat 57, Vers-chez-les-Blanc, CH-1000, Lausanne 26, Switzerland. Electronic address:
Centers for Disease Control and Prevention, MS-CO-3, 1600 Clifton Road, 30329-4027, Atlanta, USA.
US Food and Drug Administration, 5001 Campus Drive, College Park, MD, 02740, USA.
Institut Mérieux, Mérieux NutriSciences, 3 route de la Chatterie, 44800, Saint Herblain, France.
Cargill Deutschland GmbH, Cerestarstr. 2, 47809, Krefeld, Germany.
Arla Innovation Center, Agro Food Park 19, 8200, Aarhus, Denmark.
Laboratoire des Sciences du Numérique de Nantes (LS2N), CNRS UMR 6004 - Université de Nantes, 2 rue de la Houssinière, 44322, Nantes, France.
The Netherlands Organisation for Applied Scientific Research, TNO, Utrechtseweg 48, 3704 HE, Zeist, NL, the Netherlands.
Mars Global Food Safety Center, Yanqi Economic Development Zone, 101407, Beijing, China.
Fuji Oil Co., Ltd., Sumiyoshi-cho 1, Izumisano Osaka, 598-8540, Japan.
Mondelēz International, Linden 3, Bournville Lane, B30 2LU, Birmingham, United Kingdom.
Tokyo University of Marine Science & Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan.
Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
Unilever Research & Development, Postbus, 114, 3130 AC, Vlaardingen, the Netherlands.
Gastrointestinal Bacteria Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5EQ, United Kingdom. Electronic address:


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 focus of this review is on the recent use and future potential of NGS in food microbiology and on current challenges. Guidance is provided for new users, such as public health departments and the food industry, on the implementation of 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.


Data sharing; Food safety and quality; Implementation; Metabarcoding; Metagenomics; Microbiology; Next generation sequencing; Whole genome sequencing


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