Monitoring the use of whole-genome sequencing in infectious disease surveillance in Europe 2015–2017

Technical report
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European Centre for Disease Prevention and Control. Monitoring the use of whole-genome sequencing in infectious disease surveillance in Europe. Stockholm: ECDC; 2018.

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The results of the 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.

Whole-genome sequencing (WGS) provides higher resolution and accuracy than classical molecular typing methods contributing to a better understanding of infectious disease and drug resistance transmission patterns and thereby improving the effectiveness of interventions for their control.

Despite these advantages, challenges with the costs and lack of expertise may limit its use by public health laboratories. Moreover, further harmonisation for bioinformatic analysis, smart and secure information technology solutions for WGS data storage and sharing, and trained staff with new skills mixes will ensure that genomic epidemiology translates into real-life infection control and prevention.

Executive summary

Whole Genome Sequencing (WGS) coupled with epidemiological and environmental investigations delivers ultimate resolution for detecting and analysing transmission routes and tracing sources of epidemic infections as well as assessing microbial virulence and antimicrobial drug resistance determinants. WGS-based typing and phenotype prediction has therefore become an essential tool for public health surveillance and molecular epidemiology of infectious diseases and antimicrobial drug resistance.

Since 2015, the ECDC National Microbiology Focal Points have been monitoring the level of implementation of WGS-based typing for national public health surveillance and investigation of prioritised diseases across the European Union (EU) and European Economic Area (EEA). The 2017 survey aims to take stock of EU/EEA national plans and technical capacity for use of WGS in public health surveillance operations. This information update will be essential for the revision of ECDC’s roadmap on disease priorities for molecular typing integration into surveillance and epidemic preparedness. It will also guide ECDC action to support equitable public health access to genomicbased typing methods across the EU/EEA.

All 30 EU/EEA countries participated in the 2017 survey. The vast majority of national public health reference laboratories had access to WGS-based typing for public health applications. Illumina was the most frequently used technology, followed by Ion Torrent technology. The access to bioinformatics expertise for routine WGS data analysis was reported as a common limiting factor. By mid-2017, two-thirds of the EU/EEA countries were using WGS analysis, either as first- or second-line typing method for surveillance of the pathogens and antibiotic resistance issues identified as EU priorities. The sampling frame used and the bioinformatics analysis varied according to the pathogen/resistance issue and the country. Core genome multi-locus allelic profiling was the most frequently used analytical approach to genotyping bacterial genomes, suggesting that there is potential bioinformatics pipeline and nomenclature compatibility. Further capacity development for WGS-based typing is ongoing, with 29 countries either using or planning to start genomic surveillance operations by 2019.

Building upon this tremendous opportunity, ECDC will help to consolidate and harmonise WGS-based typing methods to enable pan-EU genomic surveillance and multi-country outbreak investigations by developing secure and flexible sequence and epidemiological data exchange, management and analysis systems  

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News

Rapid progress in public health implementation of whole-genome sequencing across the EU/EEA

News story -

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.