Use of next‐generation sequencing in microbial risk assessment

food safety, next-generation sequencing, whole genome sequencing, microbial riskassessment, Illumina, Oxford Nanopore Technologies, MiSeq, MinION
First published in the EFSA Journal
27 August 2018
6 July 2018
Special Issue

This report is funded by EFSA as part of the EU‐FORA programme.

Note: The full opinion will be published in accordance with article 8(6) of Regulation (EC) No 1831/2003 once the decision on confidentiality, in line with article 18(2) of the Regulation, will be received from the European Commission.


Despite the ever increase in rigorous control and monitoring measures to assure safe food along the entire farm‐to‐fork chain, the past decade has also witnessed an increase in microbial food alerts. Hence, research on food safety and quality remain of utmost importance. Complementary, and at least as important, is the necessity to be able to assess the potential microbial risks along the food chain. Risk assessment relies on sound scientific data. Unfortunately, often, quality data are limited if not lacking. High‐throughput tools such as next‐generation sequencing (NGS) could fill this gap. NGS approaches can be used to generate ample qualitative and quantitative data to be used in the risk assessment process. NGS applications are not new in food microbiology with applications ranging from pathogen detection along the food chain, food epidemiology studies, whole genome analysis of food‐associated microorganisms up to describing complete food microbiomes. Yet, its application in the area of microbial risk assessment is still at an early stage and faces important challenges. The possibilities of NGS for risk assessment are ample, but so are the questions on the subject. One of the major strengths of NGS lies in its capacity to generate a lot of data, but to what extend can this wealth be of use in hazard identification, hazard characterisation and exposure assessment to perform a sound risk characterisation, which in turn will make it possible to take substantiated risk management decisions.

eu-fora [at]
EFSA Journal 2018;16(S1):e16086