Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms

whole genome sequencing, metagenomics, microbial risk assessment, source attribution, antimicrobial resistance, typing of food‐borne pathogens, food‐borne outbreak investigation
First published in the EFSA Journal
3 Diciembre 2019
23 Octubre 2019
Scientific Opinion


This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne pathogens. WGS offers the highest level of bacterial strain discrimination for food‐borne outbreak investigation and source‐attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial‐temporal factors and the detection of multidirectional transmission and pathogen–host interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non‐culturable, difficult‐to‐culture or slow‐growing microorganisms, for tracking of hazard‐related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin‐producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGS‐based genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross‐border outbreaks and for the development of international standardised risk assessments of food‐borne microorganisms.

Panel members at the time of adoption

Ana Allende, Avelino Alvarez‐Ordóñez, Declan Bolton, Sara Bover‐Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Kostas Koutsoumanis, Roland Lindqvist, Maarten Nauta, Luisa Peixe, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis and Elisabetta Suffredini.
Panel on Biological Hazards
biohaz [at] efsa.europa.eu
EFSA Journal 2019;17(12):5898
Question Number
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