The Swiss Pathogen Surveillance Platform (SPSP) has collected, curated, processed and shared openly more than 160’000 SARS-CoV-2 genomic datasets and associated metadata, making Switzerland the 5th world-wide contributor of SARS-CoV-2 open data. It is now time to make SPSP also available for clinical bacterial data.

SPSP is now part of a Swiss-wide project bringing together all the University clinical microbiology laboratories (SPHN NDS IICU). Within this project, data providers will submit to SPSP bacterial genomic data from positive blood cultures of Intensive Care Unit (ICU) patients and bacterial MALDI-TOF profiles from all patients of Swiss University Hospitals ICUs, to be then shared to open data repositories. While the former represents a few thousand genomic datasets per center and per year, the latter corresponds to a few thousands datasets per center and per week. In this context, entries into SPSP should be automated in a robust fashion, similar to the data sharing mechanisms already in place with
anresis.ch for phenotypic resistance data.

Here, we aim to (I) set up automated interfaces to allow University clinical microbiology laboratories to robustly prepare high quality data by automatically extracting the required fields from their internal information systems and submitting them to SPSP by a standardized procedure; and (II) implement a bidirectional interface between anresis and SPSP for automatic data exchanges between these platforms, thereby enabling interoperable data integrations and making unique FAIR datasets accessible to the research community.