Whole Genome Sequencing

Inter-EURLs Working Group on NGS

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

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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.

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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. 

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• Overview of conducted and planned PTs - curated by EURL Antimicrobial Resistance
• Reference Whole Genome Sequencing collection - curated by EURL Salmonella​
• Guidance document for WGS-laboratory procedures - curated by EURL Parasites
• Bioinformatics tools for basic analysis of Next Generation Sequencing data - curated by EURL VTEC
  
• Guidance document for cluster analysis of whole genome sequence data - curated by EURL Campylobacter
• Guidance document for NGS-Benchmarking - curated by EURL Listeria
• Inventory of training supports - curated by EURL Coagulase Positive Staphylococci
• Survey on the use of NGS across the NRLs networks - curated by EURL VTEC
• Supporting document for preparing high quality DNA for Whole Genome Sequencing - curated by EURL VTEC

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

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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.

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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

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

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"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