Collection and analysis of whole genome sequencing data from food-borne pathogens and other relevant microorganisms isolated from human, animal, food, feed and food/feed environmental samples in the joint ECDC–EFSA molecular typing database
This report identifies and compares potential platforms/solutions for the set-up and running of a joint ECDC–EFSA database to collect and analyse whole genome sequencing (WGS) data for Listeria monocytogenes, Salmonella and Escherichia coli. In particular, WGS introduces the need for specific components for storage and analysis of these data.
Proficiency test for Listeria monocytogenes whole genome assembly 2018
This report presents the results of a proficiency test to evaluate the inter-laboratory reproducibility and portability of Listeria monocytogenes (Lm) genome assemblies in the EU/EEA.
Whole genome sequencing: new ECDC framework suggests priority diseases and implementation options
Whole genome sequencing (WGS) is a fast-moving technology, but the pace of change vary between pathogens/diseases and European Union countries. In a new report, ECDC proposes to prioritise the implementation of WGS depending on disease and public health application.
Call for scientific collaboration to support genomic-based surveillance of Neisseria gonorrhoeae-antimicrobial resistance at EU-level
ECDC is looking to establish a scientific collaboration with an organisation which can perform whole genome sequencing (WGS) of Neisseria gonorrhoeae, carry out related data analyses, share results of the analyses with ECDC and the participants of the European Gonococcal Antimicrobial Surveillance Programme as well as visualise the results.
Multi-country outbreak of Listeria monocytogenes sequence type 8 infections linked to consumption of salmon products
A multi-country outbreak of 12 listeriosis cases caused by Listeria monocytogenes sequence type (ST) 8 has been identified through whole genome sequencing (WGS) analysis in three EU/EEA countries: Denmark (6 cases), Germany (5) and France (1).
Monitoring the use of whole-genome sequencing in infectious disease surveillance in Europe 2015–2017
The results of the third pan-EU/EEA survey presented in this report showed that by mid-2017 the vast majority of national public health reference laboratories in EU/EEA countries had access to whole genome sequencing based typing of diverse microbial pathogens for investigations of infection and drug resistance transmission.
Rapid progress in public health implementation of whole-genome sequencing across the EU/EEA
The EU/EEA countries are making great progress in the implementation of whole-genome sequencing (WGS) technology for outbreak investigation and surveillance. With a harmonisation of standards, this will enable exchange of WGS-derived data across the EU/EEA as prioritised in the ECDC Roadmap for molecular surveillance and improve disease control and prevention in Europe.
Joint Rapid Outbreak Assessment: Multi-country outbreak of Salmonella Agona infections linked to infant formula
This document provides an assessment of the public health risk associated with a multi-country outbreak of Salmonella Agona associated with consumption of potentially contaminated infant formula from France.
Multidrug-resistant tuberculosis in migrants, multi-country cluster - 3rd update, 13 April 2017
A multi-country cluster of multidrug-resistant tuberculosis (MDR TB) involving 28 migrants has been delineated by whole genome sequencing (WGS) in migrants recently having arrived from countries in the Horn of Africa.