The technology for whole-genome sequencing (WGS) is becoming increasingly efficient and cost-competitive for diagnostic and surveillance purposes. A recent survey shows that the vast majority of national public health reference laboratories in EU/EEA countries now have access to WGS-based typing of diverse microbial pathogens for investigations of infection and drug resistance transmission. Two-thirds of the countries were routinely using WGS in 2017 for national surveillance of at least one human pathogen. Moreover, more non-user countries were planning to use WGS within three years.

With a harmonisation of standards, the progress made should enable WGS-derived data exchange across the EU/EEA in the medium-term. Together with its partners, ECDC will contribute to identifying solutions and broadening capacities in these areas, with the primary aim of facilitating inter-operability with EU and national surveillance and outbreak response programmes.

Whole-genome sequencing (WGS) provides higher resolution and accuracy than traditional molecular typing methods, such as PFGE or MLVA. This contributes to a better understanding of infectious disease and antimicrobial drug resistance transmission patterns, subsequently improving the efficacy of interventions for their control.