Project description

Antimicrobial resistance (AMR) represents an escalating global health threat, often propagated by mobile genetic elements such as plasmids that facilitate horizontal gene transfer (HGT). Traditional surveillance methods focused on chromosomal data are increasingly insufficient to detect and track multiclonal outbreaks – such as those involving carbapenemase-producing Enterobacteriaceae (CPE) – where resistance determinants can spread across unrelated strains. To address these challenges, this project aims to enhance the Swiss Pathogen Surveillance Platform (SPSP) with novel bioinformatics tools specifically designed for plasmid characterization, resistance profiling, and integrated outbreak analysis.

The technical foundation spans Work Packages 2–5: validating genotype-to-phenotype correlations in collaboration with ANRESIS (WP2), improving long-read sequencing for plasmid resolution (WP3), integrating plasmid analysis tools into the SPSP infrastructure (WP4), and contextualizing AMR transmission events using phylogenetic and plasmid data (WP5). These developments converge in WP6, which plays a pivotal role in demonstrating the real-world value of the platform. WP6 will apply the developed tools to use cases such as carbapenemase-producing Gram negative bacteria , evaluating their performance within and across sectors, across geographic regions, and under real life conditions. It will also define the thresholds for detecting significant clusters, assess the limitations of automated pipelines, and establish criteria for when expert review is required.

Coordinated by WP1 and supported by WP7’s focus on sustainable data curation and sharing, this project contributes to a scalable and actionable surveillance framework under a One Health perspective, with SPSP positioned as a national resource for outbreak response and AMR monitoring.

List of Co-Applicants

• Aitana Neves – SIB Swiss Institute of Bioinformatics
• Adrian Egli, Tim Roloff – University of Zurich
• Peter Keller – University Hospital Basel
• Stephen Leib, Alban Ramette, Vincent Perreten (VetSuisse), Andreas Kronenberg (ANRESIS) – University of Bern
• Gilbert Greub, Dominique Blanc – University Hospital Lausanne
• Jacques Schrenzel – University Hospital Geneva
• Laurent Poirel (NARA) – University of Fribourg

Funding source

Subvention from the Federal Office of Public Health and Federal Food Safety and Veterinary Office