Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms
Abstract 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 sour...
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doaj-10be660a5b8843b4ab5cb9cb6cde3bed2021-05-02T06:57:34ZengWileyEFSA Journal1831-47322019-12-011712n/an/a10.2903/j.efsa.2019.5898Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganismsEFSA Panel on Biological Hazards (EFSA BIOHAZ Panel)Kostas KoutsoumanisAna AllendeAvelino Alvarez‐OrdóñezDeclan BoltonSara Bover‐CidMarianne ChemalyRobert DaviesAlessandra De CesareFriederike HilbertRoland LindqvistMaarten NautaLuisa PeixeGiuseppe RuMarion SimmonsPanagiotis SkandamisElisabetta SuffrediniClaire JenkinsBurkhard MalornyAna Sofia Ribeiro DuarteMia TorpdahlMaria Teresa da Silva FelícioBeatriz GuerraMirko RossiLieve HermanAbstract 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.https://doi.org/10.2903/j.efsa.2019.5898whole genome sequencingmetagenomicsmicrobial risk assessmentsource attributionantimicrobial resistancetyping of food‐borne pathogens |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
EFSA Panel on Biological Hazards (EFSA BIOHAZ Panel) Kostas Koutsoumanis Ana Allende Avelino Alvarez‐Ordóñez Declan Bolton Sara Bover‐Cid Marianne Chemaly Robert Davies Alessandra De Cesare Friederike Hilbert Roland Lindqvist Maarten Nauta Luisa 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 |
spellingShingle |
EFSA Panel on Biological Hazards (EFSA BIOHAZ Panel) Kostas Koutsoumanis Ana Allende Avelino Alvarez‐Ordóñez Declan Bolton Sara Bover‐Cid Marianne Chemaly Robert Davies Alessandra De Cesare Friederike Hilbert Roland Lindqvist Maarten Nauta Luisa 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 Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms EFSA Journal whole genome sequencing metagenomics microbial risk assessment source attribution antimicrobial resistance typing of food‐borne pathogens |
author_facet |
EFSA Panel on Biological Hazards (EFSA BIOHAZ Panel) Kostas Koutsoumanis Ana Allende Avelino Alvarez‐Ordóñez Declan Bolton Sara Bover‐Cid Marianne Chemaly Robert Davies Alessandra De Cesare Friederike Hilbert Roland Lindqvist Maarten Nauta Luisa 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 |
author_sort |
EFSA Panel on Biological Hazards (EFSA BIOHAZ Panel) |
title |
Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms |
title_short |
Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms |
title_full |
Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms |
title_fullStr |
Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms |
title_full_unstemmed |
Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms |
title_sort |
whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms |
publisher |
Wiley |
series |
EFSA Journal |
issn |
1831-4732 |
publishDate |
2019-12-01 |
description |
Abstract 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. |
topic |
whole genome sequencing metagenomics microbial risk assessment source attribution antimicrobial resistance typing of food‐borne pathogens |
url |
https://doi.org/10.2903/j.efsa.2019.5898 |
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