Useful information 21/03/2024 12780 21/03/2024
Measurement uncertainty This page provides the output of a working group of the EURLs for Campylobacter, Coagulase Positive Staphylococci and Listeria monocytogenes 13/01/2023 11543 08/09/2022
HOW-TO TRANSFER YOUR SEQUENCES TO THE EURL? The EURL proposes to upload your data on our FTP server. Recommanded FTP sofware: FileZilla Credentials: Protocol: FTP File Transfer Protocol Host: swiftp.anses.fr     Port: 21 Encryption: Require implicit FTP over TLS Logo Type: Normal User : ftp-staphylocoques Password: Sta-125-5MUvNkSvGkY  Tutorial: From your computer files (left panel) drag and drop the files in the FTP directory (right panel). 13/04/2022 11259 12/04/2022
Starflow : online service for the analysis of WGS datasets from S. aureus Get the user guide: link This service allows to characterise the strains you have found in outbreak investigation, surveillance and/or research activities providing: assembly with quality criterion MLST typing Staphylococcal Enterotoxin profile cgMLST typing Process: 1. collect your sequences 2. fill out the transfer form 3. create the zip file 4. upload your NGS data 5. StarFlow pipeline 6. Report provided online   21/05/2024 9579 14/04/2020
How-to transfer your sequences to the EURL? The EURL proposes to upload your data on our FTP server. Recommanded FTP sofware: FileZilla Credentials: host: swiftp.anses.fr login: ftp-eurllmsup password: 9CMNHgFMKbQH3OITWT2c port: 21 Tutorial: From your computer files (left panel) drag and drop the files in the FTP directory (right panel). 25/02/2020 9499 25/02/2020
CPS Calendar 2025: 19th June: 16th meeting of the Inter EURLs WG on NGS 17-18 June: Joint NGS training organised by the Inter EURLs WG on NGS at Maisons-Alfort 1-2 April: 19th Annual Workshop of EURL CPS 7th March: 10th meeting of the WG on typing methods 2024: 10th December: 15th meeting of the Inter EURLs WG on NGS 15th-16th October: EURL WGS training at the NRL in Slovenia 17th October: meeting of Inter EURLs WG on NGS guidance document on Quality Check of NGS data 26 June: 14th meeting of the Inter EURLs WG on NGS  25-26 June: Joint NGS training organised by the Inter EURLs WG on NGS at Uppsala  11-13 June: 18th Annual Workshop of EURL CPS 9 April: 9th meeting of the working group on typing methods 2023: 13 December: 13th meeting of the Inter EURLs WG on NGS  23 November: 8th meeting of the working group on typing methods 24-26 October: 17th Annual Workshop of EURL CPS 29 September: webinar on “Proficiency Tests on NGS: approaches in use at the European Union Reference Laboratories” 5-6 September: "Science meets Policy" conferences co-organised by EFSA and the Inter EURLs WG on NGS 30 June: 7th meeting of the working group on typing mehods 22 June: 12th meeting of the Inter EURLs WG on NGS 20-21 June : Joint NGS training organised by the Inter EURLs WG on NGS at Bilthoven 2nd March: meeting of the Inter EURLs WG on NGS - Discussion on Proficiency Tests 21st February: launching of the inter-laboratory comparison on the wet lab of Whole Genome Sequencing within the Working group on typing methods 2022: 6th December: 11th meeting of the Inter EURLs WG on NGS in Bruxelles 25th October: 6th meeting of the EURLs WG on typing methods 20th -21th October: EURLs joint-training on measurement uncertainty 5th-6th October: EURL WGS training at the NRL in Hungary 26th September: PT on CPS enumeration  15th - 16th September EURL SE training: Italian project of implementation ELISA specific ES 5th and 6th September: Training session on EN ISO 19020 22nd June: 10th meeting of the Inter EURLs WG on NGS 13th-14th June: Joint NGS training in Rome organised by the Inter EURLs WG on NGS 30th May - 1 June: 16th workshop of the EURL/NRLs  27th April: 7th meeting of the WG 25 on ISO 23418 (WGS) 29th March: PT staphylococcal enterotoxins detection 3rd March: Inter EURLs WG on NGS meeting: organization of joint trainings 1st Fevrier : 5th meeting of the EURLs WG on typing methods 2021: 14th December: 9th Inter EURLs WG on NGS meeting 18th October: PT on the CPS enumeration 22nd October: 4th meeting of the EURLs WG on typing methods 4th October: 15th workshop of the EURL/NRLs (enumeratio and typing) 30th June: I8th nter EURLs WG on NGS meeting 13th April: 6th meeting of the WG 25 on ISO 23418 (WGS) 4th May: 15th workshop of the EURL/NRLs 2020: PT on the detection of staphylococcal enterotoxin 26-28 June: workshop of the EURL/NRLs 2019: PT on the detection of staphylococcal enterotoxin 26-28 June: workshop of the EURL/NRLs   14/05/2025 7438 12/12/2018
Enumeration 20/12/2024 4016 10/04/2015
CPS Characterisation Detection of Staphylococcal enterotoxins (SE): list, sequence of se genes, sequence of SE proteins WGS pipeline: 1- StarFlow 2- Galaxy Workflow 1 Whole genome sequencing (WGS) protocols and methods: Recommendations for WGS wet lab and dry lab methods Protocol for manual DNA extraction and semi automated DNA extraction Protocol for Illumina library preparation on a Miseq Comparison of WGS with classical typing methods (Vingadassalon et al 2024) SNP threshold for the analysis of CPS outbreaks (Duchez et al 2025) Genomic analysis tool for the detection of enterotoxins coding genes (NAuRA - Merda et al 2019) Conventional multiplex PCR (sea to see and ser and seg to sej and sep) Multiplex RT-PCR: LSA-INS-1294   13/06/2025 3992 03/04/2015
Extraction by dialysis concentration step Step by step 29/01/2015 3691 29/01/2015
Working areas Bacterial Detection enumeration (soon) Staphylococcal enterotoxins Characterisation (soon) 22/10/2014 3398 22/10/2014

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