Introduction

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 at (supra-)national level to strengthen WGS capacities have led to the need for a eHealth information infrastructure. Hereby, the integration of genomic, clinical and epidemiological data is crucial.

Materials & 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 NRC 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.

Discussion

The Salmonella NRC platform allows 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 MicroReact allowing a dynamic visualization of Salmonella phylogeny and infections over time. The integrated display 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, to facilitated outbreak investigation, an automated detection tool generates alerts when newly added isolates cluster together within a defined distance (less than 5 allelic differences using cgMLST) and time-lapse (minimum 5 cases identified within 2 months). Testing this tool over the course of 2024, during which 2514 isolates were received at the NRC and 1088 were sequenced, we recorded a total of 18 alerts corresponding to potential outbreaks, including 7 clusters of S. Enteritidis, 9 clusters of S. (Monophasic) 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.