The ambitious plan to integrate genomics and patient data in the surveillance of infectious disease and AMR in Belgium: Experiences from be.Prepared

The planned phasing out of the BioNumerics™ software package (Biomérieux) has been causing headaches in public health and national reference laboratories. Faced with the challenge of retaining their phylogenetic capacity and large historical data collections, many labs have turned to locally implemented or cloud-based commercial alternatives, such as Ridom GmbH (SeqSphere™) or 1928 Diagnostics AB, to continue their surveillance. However, this was not the path chosen in Belgium.

The Belgian Public Health Institute (Sciensano) conceptualized an overarching infrastructure to integrate genomics and epidemiological data. Supported by three years of funding from the EU’s Health Emergence Response Authority, Sciensano started to develop its ‘be.Prepared’ platform. This architecture intended to integrate pathogen and patient data from clinical labs from the moment of validation, with genome data from the reference labs and available patient data, all the way to reporting to regional and international health actors. Central to the system is a cloud-based bioinformatics platform with locally implemented versions of BigsDB and MicroReact.