Background

Over the last decade, whole-genome sequencing (WGS)-based surveillance has demonstrated its usefulness for public health applications such as outbreak investigation, detection of antimicrobial resistance, or pathogen characterization for vaccine development. Substantial investments have been made at (supra-)national level to strengthen WGS capacities, and have led to the need for a eHealth information infrastructure that could be used for a wide range of pathogens. Hereby, the integration of genomic, clinical and epidemiological data is crucial.

Methods

be.Prepared, the Belgian Preparedness Architecture for Infectious Diseases, is a development funded by the European Union under the HERA-Incubator-WGS and HERA-BE-WGS projects, in which several platforms are being implemented to integrate pathogen and health data from multiple surveillance systems. Among others, a platform based on the architecture of BIGSdb was developed to support the National Reference Centre for Salmonella in Belgium in conducting surveillance of Salmonella cases. This NRC usability platform links together microbial genomic data  with patient clinical and epidemiological data.

Results  & Discussion

The Salmonella NRC platform allows an intuitive and user-friendly visualization of Salmonella cases in Belgium. It displays in a single interface all the results of nominative patient data (such as age, sex or location), secondary metadata (including predicted resistance genes, serotyping, assembly statistics) and features a selection of third-party tools such as GrapeTree and MicroReact allowing a dynamic visualization of Salmonella phylogeny and infections over time. The integrated display through trees, maps, timelines and tables provides a valuable solution for pathogen surveillance, helping to understand the transmission routes of Salmonella, the spread of high-risk clones or the emergence of antimicrobial resistance.

Moreover, an automated detection tool generates alerts when newly added isolates cluster together within a defined distance (less than five allelic differences using cgMLST) and time-lapse (minimum five cases identified within two months), leading to facilitated outbreak investigation. Testing this tool over the course of 2024, during which 2461 isolates were received at the NRC and 1065 underwent WGS analysis, we recorded a total of 21 alerts corresponding to potential outbreaks, including 11 clusters of S. Enteritidis, three clusters of S. Typhimurium, six clusters of monophasic S. Typhimurium, one cluster of S. Ball, and one cluster of S. Napoli.

Overall, this pilot platform represents a valuable tool for day-to-day genomic surveillance, and will be extended in the future to accommodate additional pathogens.