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

2019; Wiley; Volume: 17; Issue: 12 Linguagem: Inglês

10.2903/j.efsa.2019.5898

1831-4732

Kostas Koutsoumanis, Ana Allende, Avelino Álvarez‐Ordóñez, Declan Bolton, Sara Bover‐Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Luísa Peixe, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Claire Jenkins, Burkhard Malorny, Ana Sofia Ribeiro Duarte, Mia Torpdahl, Maria Teresa da Silva Felício, Beatriz Guerra, Mirko Rossi, Lieve Herman,

Bacillus and Francisella bacterial research

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