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. 

Webinar: 'Proficiency Tests on Next Generation Sequencing: approaches in use at the European Union Reference Laboratories'(29 September 2023)​​:

According to Regulation (EU) 2017/625 (Article 101), the National Reference Laboratories shall, where appropriate, organize inter-laboratory comparative testing or Proficiency Tests between official laboratories.

This event, organized by the Inter EURLs WG on NGS, aimed at presenting the approaches used by EURLs AMR, Campylobacter, Listeria monocytogenes, Salmonella and VTEC for Proficiency Tests on NGS, to share experiences learnt and serve as guidelines for the organization of Proficiency Tests on NGS at the Member State level



(PDF document, 0.6 MB)



By Valeria Michelacci

(PDF document, 0.4 MB)


EURL Antimicrobial Resistance

By Susanne Karlsmose Pedersen

(PDF document, 1.5 MB)


EURL Campylobacter

By Bo Segerman

(PDF document, 0.4 MB)


EURL E. coli 

By Valeria Michelacci

(PDF document, 0.8 MB)


EURL Listeria monocytogenes

By Maroua Sayeb

(PDF document, 0.7 MB)


EURL Salmonella

By Wilma Jacobs Reitsma, Angela van Hoek and Kirsten Mooijman

(PDF document, 1.3 MB)

"Science meets Policy" conference 2023: 'Using Next Generation Sequencing to tackle foodborne threats' (September 5-6, 2023)​​ - link to video recordings and presentations

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


EU Food Safety Policy and NGS

By Martial Plantady, EU Commission

(PDF document, 3.1 MB)


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

By Valentina Rizzi, EFSA

(PDF document, 3.0 MB)


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

By Saara Kotila, ECDC

(PDF document, 1.3 MB)


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

By George Haringhuizen, RIVM

(PDF document, 2.3 MB)


The use of Genomics in One Health AMR Surveillance

By Patrick McDermott, US-FDA

(PDF document, 6.0 MB)


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