ECDC releases opinion on whole genome sequencing

The European Centre for Disease Prevention and Control (ECDC), along with member states, released an opinion this week on whole genome sequencing (WGS) for public health surveillance.

Whole genome sequencing is a laboratory process that determines the complete DNA sequence of an organism’s genome at a single time, which provides for more accurate pathogen identification, antimicrobial resistance profiling, transmission tracking and biological risk assessment.

In its opinion, the ECDC detailed the obstacles WGS faces, ranging from differences in the sequencing platforms, inter-laboratory comparability, lack of standard bioinformatics pipelines, the definition of WGS-derived strain nomenclature, comparability with older typing techniques, and the translation of epidemiological and genomic sequence data into meaningful information for public health decision-making.

To ensure that WGS is adopted without compromising the continuity of national and European Union-level surveillance, the ECDC proposed mapping other WGS-based public health initiatives and engaging partnerships, providing guidance on and validation of WGS-based methods for surveillance, and developing and evaluating selected pilot implementation studies.

“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,” Marc Struelens, chief microbiologist at ECDC, said. “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.”