Technical consultation: ECDC strategy to harness whole genome sequencing for cross-border outbreak and surveillance

19 Nov 2015
Stockholm, Sweden
ECDC, Microbiology Coordination Section

T​he aims of the consultation were to review the draft strategy and discuss how to foster practical collaboration with European and global initiatives in this field.

The meeting, which brought together National Focal Points for Microbiology and for Surveillance, allowed to review proposals for the second edition of the ECDC roadmap for integration of molecular typing into outbreak investigation and EU surveillance. The Task Force advised ECDC on each disease proposal in terms of EU added value and technical feasibility.

Meeting report

The meeting participants concluded that use of whole genome sequencing (WGS) analysis of microbial pathogens adds value to public health. General support was offered to the ECDC strategy that envisions that in five years’ time, ECDC will have contributed to the establishment standards and 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.

The presentations from leading translational research groups and public health partners showed that a number of WGS analytical tools are now available for public health applications. ECDC was invited to be part of a global conversation towards reaching common analytical approaches and interpretation criteria for disease surveillance.

Key messages from the expert consultation were:

ECDC should:

a. foster multidisciplinary interpretation of the integrated information arising from the combination of epidemiological data and pathogen sequence characterisation to guide public health action;

b. together with its public health laboratory network partners, EFSA, and research and development projects, define the priorities and identify high impact diseases or drug resistance issues, for which genome sequence information can make a difference for public health intervention;

c. contribute to a global agreement on WGS analytical approaches, epidemiological interpretation criteria and genomic nomenclature by surveillance objective, while keeping flexibility to explore improved methods;

d. help with the multi-country evaluation of the public health effectiveness of WGS-based typing by measuring outcomes in terms of disease prevention or size of outbreaks before and after implementing it within a disease surveillance programme;

e. focus its training efforts towards developing a new, integrative “genomic epidemiology” discipline, to build a common understanding through continuous professional development.

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