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 ECDC Roadmap for molecular surveillance and improve disease control and prevention in Europe.
The technology for whole-genome sequencing (WGS) is becoming increasingly efficient and cost-competitive for diagnostic and surveillance purposes. A recent survey shows that the vast majority of national public health reference laboratories in EU/EEA countries now have access to WGS-based typing of diverse microbial pathogens for investigations of infection and drug resistance transmission. Two-thirds of the countries were routinely using WGS in 2017 for national surveillance of at least one human pathogen. Moreover, more non-user countries were planning to use WGS within three years.
With a harmonisation of standards, the progress made should enable WGS-derived data exchange across the EU/EEA in the medium-term. Together with its partners, ECDC will contribute to identifying solutions and broadening capacities in these areas, with the primary aim of facilitating inter-operability with EU and national surveillance and outbreak response programmes.
Whole-genome sequencing (WGS) provides higher resolution and accuracy than traditional molecular typing methods, such as PFGE or MLVA. This contributes to a better understanding of infectious disease and antimicrobial drug resistance transmission patterns, subsequently improving the efficacy of interventions for their control.
Molecular and genomic typing
Molecular typing of pathogens that cause infectious diseases complements the traditional epidemiological surveillance by providing appropriate discriminatory analyses to foster the rapid and early detection of widespread international outbreaks.Read more
Expert opinion on whole genome sequencing for public health surveillance
15 Aug 2016 - 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.
Microbiology laboratories provide a first line of defence against health threats from communicable diseases and antimicrobial resistance. The ECDC provides scientific advice, capacity building activities and operational support to foster capable and responsive public health microbiology services for the European Union and beyond. ECDC’s vision is that by 2022 communicable disease and antimicrobial resistance threat detection, risk assessment, public health surveillance, and response in the EU/EEA will be underpinned by reliable and comparable microbiology data, shared and used in a timely manner.Read more