Whole Genome Sequencing

Inter-EURLs Working Group on NGS

Inter-European Union Reference Laboratories Working Group on Next Generation Sequencing

The Inter-European Union Reference Laboratories (EURLs) Working Group (WG) has been established by the European Commission with the aim to promote the use of Next Generation Sequencing (NGS) across the EURLs' networks, build NGS capacity within the EU and ensure liaison with the work of the EURLs and the work of EFSA and ECDC on the NGS mandate sent by the Commission. The WG includes all the EURLs operating in the field of the microbiological contamination of food and feed and is coordinated by the EURL for E. coli.

The documents linked in this section are meant to provide guidance to the laboratories in the area of application of NGS and have been produced by the working group with the aim of being diffused to all the networks of NRLs. 


  • Overview of conducted and planned PTs - curated by EURL Antimicrobial Resistance [link to be added a.s.a.p. when the document has been through review]
  • Reference Whole Genome Sequencing collection - curated by EURL Salmonella [link to be added a.s.a.p. when the document has been through review]
  • NGS laboratory procedures - curated by EURL Parasites [link to be added a.s.a.p. when the document has been through review]
  • Bioinformatics tools for basic analysis of Next Generation Sequencing data - curated by EURL VTEC [link to be added a.s.a.p. when the document has been through review]
  • Guidance document for cluster analysis of whole genome sequence data - curated by EURL Campylobacter [link to be added a.s.a.p. when the document has been through review]
  • Guidance document for NGS-Benchmarking - curated by EURL Listeria [link to be added a.s.a.p. when the document has been through review]
  • Inventory of training supports - curated by EURL Coagulase Positive Staphylococci [link to be added a.s.a.p. when the document has been through review]
  • Survey on the use of NGS across the NRLs networks - curated by EURL VTEC [link to be added a.s.a.p. when the document has been through review]

​​Access presentations from the "Science meets Policy" conference: 'Modern technologies to enable response to crises: Next Generation Sequencing to tackle food-borne diseases (September 25, 2020)​​

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EU Food Safety Policy and NGS

By Martial Plantady, EU Commission

(PDF document, 3.1 MB)

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EFSA - State of play and future perspectives in the food safety area

By Valentina Rizzi, EFSA

(PDF document, 3.0 MB)

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ECDC - State of play and future perspectives in the public health area

By Saara Kotila, ECDC

(PDF document, 1.3 MB)

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Need for a legal framework for NGS data supporting action by the CAs

By George Haringhuizen, RIVM

(PDF document, 2.3 MB)

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The use of Genomics in One Health AMR Surveillance

By Patrick McDermott, US-FDA

(PDF document, 6.0 MB)

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