Published July 25, 2023
| Version v1
Journal article
Open
European Union Reference Laboratories support the National food, feed and veterinary Reference Laboratories with rolling out whole genome sequencing in Europe
Creators
-
1.
Istituto Superiore di Sanità
-
2.
French Agency for Food, Environmental and Occupational Health & Safety
-
3.
National Institute for Public Health and the Environment
-
4.
Technical University of Denmark
-
5.
National Veterinary Institute
- 6. Swedish Food Agency - Livsmedelsverket
Description
The Inter European Union Reference Laboratories (EURLs) Working Group on Next Generation Sequencing (NGS) involves eight EURLs for microbiological food and feed hazards and has been working since 2017 to promote the adoption of NGS by the National Reference Laboratories (NRLs) in the European Union. This work illustrates the results of the first 5 years of activity. By working together, the EURLs involved have released guidance documents for assisting NRLs in all the steps of NGS, helping the transition from classical molecular methods towards whole genome sequencing while ensuring harmonization, with the final aim of improving preparedness in the use of NGS to characterize microbial hazards and trace the sources of infection.
Notes
Short communication
Files
Michelacci_Microbial Genomics_2023.pdf
Files
(194.3 kB)
| Name | Size | Download all |
|---|---|---|
|
md5:c1fa280a41f736eda2fe31a452e0589c
|
194.3 kB | Preview Download |
Additional details
References
- The European Parliament and the Council of the European Union REGULATION (EU) 2017/625 OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 15 March 2017 on official controls and other official activities performed to ensure the application of food and feed law, rules on animal health and welfare, plant health and plant protection products, amending regulations (EC) no 999/2001, (EC) no 396/2005, (EC) no 1069/2009, (EC) no 1107/2009, (EU) no 1151/2012, (EU) no 652/2014, (EU) 2016/429 and (EU) 2016/2031 of the European Parliament and of the Council, Council Regulations (EC) No 1/2005 and (EC) No 1099/2009 and Council Directives 98/58/EC, 1999/74/EC, 2007/43/EC, 2008/119/EC and 2008/120/EC, and repealing Regulations (EC) No 854/2004 and (EC) No 882/2004 of the European Parliament and of the Council, Council Directives 89/608/EEC, 89/662/EEC, 90/425/EEC, 91/496/EEC, 96/23/EC, 96/93/EC and 97/78/EC and Council Decision 92/438/EEC. Official Journal of the European Union 2017 [Google Scholar]
- European Commission Directorate General for Health and Food Safety Request for the implementation of a One Health system for the collection and analysis of whole-genome sequencing (WGS) datafrom human and food/animal isolates; 2019 https://open.efsa.europa.eu/study-inventory/EFSA-Q-2020-00101
- ISO Technical Committee ISO/TC 34/SC 9 Microbiology ISO 23418:2022 Microbiology of the food chain — Whole genome sequencing for typing and genomic characterization of bacteria — General requirements and guidance; 2022 https://www.iso.org/standard/75509.html
- Inter-EURLs Working Group on NGS Survey on the use of NGS across the NRLs networks; 2020 https://www.iss.it/documents/5430402/0/Survey+on+the+use+of+NGS+Del8.pdf/27f19f4b-1d85-8437-6ef0-a65aac2c6617?t=1614771657671
- EURL for Escherichia coli including Shiga toxin-producing E. coli Inter-European Union Reference Laboratories Working Group on Next Generation Sequencing; 2018 https://www.iss.it/en/-/inter-european-union-reference-laboratories-working-group-on-next-generation-sequencing-1
- COMPARE COMPARE EUROPE; 2015 https://www.compare-europe.eu/
- Rene S. Hendriksen SKP, Leekitcharoenphon P, Malorny B, Borowiak M, Battisti A et al. Final Report of ENGAGE - Establishing Next Generation Sequencing Ability for Genomic Analysis in Europe EFSA supporting publication 2018; 2018 [Google Scholar]
- Llarena A-K, Ribeiro-Gonçalves BF, Silva DN, Halkilahti J, Machado MP et al. INNUENDO: A cross-Sectoral platform for the integration Ofgenomics in the surveillance of food-borne pathogens. EFSA supporting publications, EXTERNAL SCIENTIFIC REPORT. EFSA Supporting Publications 2018; 15: [View Article] [Google Scholar]
- Inter-EURLs Working Group on NGS Guidance document for WGS-laboratory procedures; 2021 https://www.iss.it/documents/5430402/0/Guidance+document+for+WGSlaboratory+procedures.pdf/2d0f3edb-7a46-754e-a0b3-2c4612b27de8?t=1637739547899
- Inter-EURLs Working Group on NGS Supporting document for preparing high quality DNA for WholeGenome sequencing; 2022 https://www.iss.it/documents/20126/6704161/Del9_guidelines_DNAquality_forPublication_23122022.pdf/ba573c2e-aa9f-9f4b-f1fe-933186c92ee6?t=1672125522440
- Inter-EURLs Working Group on NGS Bioinformatics tools for basic analysis of next generation sequencing data; 2022 https://www.iss.it/documents/20126/6704161/Del4_Tools_for_basic_analysis_forPublication_23 122022.pdf/0def662e-0195-8af2-c956-ff26d09e7ae6?t=1672125015933
- Inter-EURLs Working Group on NGS Guidance document for cluster analysis of whole genome sequence data; 2022 https://www.sva.se/media/8da546180a1a226/del5_guidelines_cluster_analysis_wg_ngs.pdf
- Inter-EURLs Working Group on NGS Overview of conducted and planned proficiency tests; 2020 https://www.eurl-ar.eu/CustomerData/Files/Folders/34-wgs/587_del1-overview-of-pts-v1-161220-corrected-002.pdf
- Inter-EURLs Working Group on NGS Reference WGS collection; 2022 https://www.eurlsalmonella.eu/sites/default/files/2023-03/Del2_Ref_Collection_v02Final_20230306.pdf
- Inter-EURLs Working Group on NGS Guidance document for WGS-Benchmarking; 2021 https://sitesv2.anses.fr/en/system/files/NGS%20EURL%20WG%20-%20Del5%20-%20Benchmarking.pdf
- Inter-EURLs Working Group on NGS Inventory of training supports; 2022 https://sitesv2.anses.fr/en/system/files/Del7_Inventory%20training%20supports%20for%20NGS_15-12-22_0.pdf
Subjects
- Listeria monocytogenes
- https://www.cabi.org/cabithesaurus/mtwdk.exe?k=default&l=60&w=201992&s=5&t=2