Expert opinion on whole genome sequencing for public health surveillance
This document sets out ECDC's five year vision for using whole genome sequencing (WGS) technology within the context of its agreed strategy and roadmap for integrating typing data into EU level surveillance and cross-border outbreak assessment.
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.
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.
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.
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).
EUSeqMyTB to set standards and build capacity for whole genome sequencing for tuberculosis in the EU
Tagliani, E., Cirillo, D.M., Ködmön, C., van der Werf, M.J.
Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015
Walle, I.V., Björkman, J.T., Cormican, M., Dallman, T., Mossong, J., Moura, A., Pietzka, A., Ruppitsch, W., Takkinen, J., Mattheus, W., Christova, I., Maikanti-Charalampous, P., Karpíšková, R., Halbedel, S., Nielsen, E.M., Koolmeister, M., Mandilara, G., Torreblanca, R.A., Salmenlinna, S., Lecuit, M., Leclercq, A., Damjanova, I., Delappe, N., Sigmundsdóttir, G., Gattuso, A., Griškevičius, A., Ragimbeau, C., Franz, E., Brandal, L.T., Kuch, A., Borges, V., Caplan, D., Jernberg, C., Alm, E., Trkov, M., Tkacova, E., Grant, K.
ECDC strategic framework for the integration of molecular and genomic typing into European surveillance and multi-country outbreak investigations
This strategic framework document presents a proposed list of priority pathogens/diseases and outlines technical implementation options for the medium-term integration (2019–2021) of molecular/genomic typing information into EU-level surveillance and multi-country outbreak investigations.
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.
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.