The technology was accessible to public health laboratories in 19 countries as of July last year.
WGS-based typing was used in 10 countries for national surveillance of one or more diseases, and in 18 for outbreak investigations.
A survey also found 18 countries were planning to implement Whole Genome Sequencing (WGS) within the next three years.
The top three surveillance targets for national WGS-based surveillance are Carbapenem-resistant Enterobacteriaceae (CRE), influenza virus and N. meningitides.
The comments were made in an expert opinion on WGS for public health surveillance from the European Centre for Disease Prevention and Control (ECDC).
Drawbacks and positives to WGS adoption
There has been a shift to Next-Generation Sequencing technology to replace DNA restriction/MLVA typing techniques and classical (Sanger method) single gene sequencing techniques.
ECDC said WGS will be adopted in phases to not compromise national or EU-level surveillance, outbreak investigation or risk assessments during transition from earlier technologies, which will occur at different speeds across the EU.
WGS has transformed public health surveillance and outbreak investigations by more accurate pathogen identification, antimicrobial resistance profiling, transmission tracking and biological risk assessment.
Obstacles range from differences in the sequencing platforms, inter-laboratory comparability, lack of standard bioinformatics pipelines, definition of WGS-derived strain nomenclature, comparability with older typing techniques, and translation of epidemiological and genomic sequence data into meaningful information for public health decision-making.
Cost assessments among EU laboratory networks have shown WGS analysis to offer reagent cost-competitive and labour-efficient alternatives to conventional epidemiological typing techniques for foodborne bacterial pathogens.
WGS can also produce results with relatively similar turn-around times to other typing techniques, depending on the laboratory throughput and processing workflows.
However, work on how to translate genomic data into meaningful information for public health decision-making is still incomplete.
Technical limitations of WGS-based typing include the complexity and reproducibility of sequence data produced.
“Firstly, the sequencing platforms currently used differ in terms of the range of quality control and this may influence the accuracy and inter-laboratory comparability of sequence data.
“Secondly, standard bioinformatics pipelines have not yet been defined and accepted for the consistent assembly of draft genomes and annotation of the WGS- derived genotypic markers based on a pathogen-specific nomenclature meeting disease-specific surveillance objectives.
“Another potential limitation of WGS typing for some diseases is the lack of backward compatibility with typing systems such as PFGE and MLVA.”
ECDC to foster application
ECDC will organise ring trials to test the multi-centre comparability of WGS data production and analysis within EU disease laboratory networks, as part of pilot studies.
If this is effective, it will then organise EQA exercises for routine WGS-based typing of priority pathogens.
It is anticipated that WGS-based surveillance of listeriosis will be operational with volunteer Member States from 2018 onwards.
The agency will work with the European Food Safety Authority (EFSA) on joint nomenclature, databases and surveillance systems in a ‘one-health’ approach to foodborne pathogens.
It will also liaise with experts in the clinical microbiology field and industry producing genome sequencing technologies and bioinformatics tools to understand and adapt to the changing landscape of infectious disease diagnostics and surveillance.
Marc Struelens, ECDC’s chief microbiologist, said: "In five years’ time, ECDC should have contributed to establish standards and manage systems enabling the EU-wide use of WGS as the method of choice for typing of microbial pathogens, replacing other methods.
"This will improve the accuracy and effectiveness of disease surveillance, outbreak investigation and evaluation of prevention policies by enhanced assessment of disease and drug resistance transmission dynamics."