This report summarises the progress made in the areas of EU-wide enhanced molecular typing for disease surveillance, genomic surveillance, and multi-country outbreak support. It also documents how Member States use Whole Genome Sequencing (WGS) in public health operations and reviews the current evidence for the effectiveness of WGS.
The proposed strategic framework sets out a revised list of priority pathogens/diseases for medium-term integration in 2019–2021. Over this period, ECDC proposes to prepare for and/or implement support to multi-country outbreak investigations, continuous EU surveillance, and sentinel surveillance. Depending on preparedness for reporting of high-quality sequence data, the following applications and pathogens are particularly relevant:
- Support to multi-country outbreak investigations through sequence-based typing: Campylobacter spp., Clostridium difficile, hepatitis A virus, Legionella spp., Listeria monocytogenes, multidrug-resistant Mycobacterium tuberculosis (MDR TB), Neisseria meningitidis, Salmonella enterica, Shiga-toxin producing E. coli, West Nile virus and emerging multi- or extensively drug-resistant (MDR or XDR) bacteria, new pathogens or new modes of transmission of healthcare-associated or community pathogens.
- EU-wide sequence-based continuous surveillance: influenza virus, Listeria monocytogenes, MDR TB, Neisseria meningitidis, Salmonella enterica and Shiga-toxin producing E. coli.
- Sentinel surveillance or surveys: antibiotic-resistant Neisseria gonorrhoeae, Bordetella pertussis, carbapenem- or colistin-resistant Enterobacteriaceae, carbapenem-resistant Acinetobacter baumannii, HIV-transmitted drug resistance, and Streptococcus pneumoniae.
The report further outlines the technological steps that are necessary to develop an integrated analytical framework and operational platform that combine sequence-based typing data with epidemiological data at the European level.
The strategic framework was revised following comments from National Focal Points for Microbiology and Surveillance (October 2018) and the ECDC Advisory Forum (February 2019).