Universitätsspital Basel
Universität Basel
Swiss Institute of Bioinformatics
Centre hospitalier universitaire vaudois
Hôpitaux Universitaires de Genève
Vetsuisse-Fakultät
Universitätsspital Basel
Universität Basel
Swiss Institute of Bioinformatics
Centre hospitalier universitaire vaudois
Hôpitaux Universitaires de Genève
Vetsuisse-Fakultät
Universitätsspital Basel
Universität Basel
Swiss Institute of Bioinformatics
Centre hospitalier universitaire vaudois
Hôpitaux Universitaires de Genève
Vetsuisse-Fakultät

Swiss Pathogen Surveillance Platform (SPSP)

SNSF NRP72 project

The project aims at building a Swiss multi-center pathogen surveillance platform, based on whole genome sequencing data of multi-drug resistant (MDR) bacteria. Starting with MRSA as a model, the platform will ultimately be expanded to other pathogens (bacteria and viruses). We anticipate that a shared surveillance platform between human and veterinary medicine, including environmental and food isolates in the future, will enable detailed transmission and outbreak surveillance of pathogens, with actionable results for public health policy.

About the NRP project

With the 3-years funding, we will develop an online platform based on NextStrain and PanGenome in order to track transmission events between humans, animals and the environment.

In contrast to existing efforts, our project envisions near real-time surveillance, including the automated modelling of transmission events, epidemiological warning functions, and linkage with high-resolution geographical data.

SPSP workflow

Envisioned benefits

A Swiss-wide one-health consortium

Centers for the proof-of-concept study:

SPSP proof-of-concept study centers

It is planned to open the platform to other centers and institutions after the first phase.

Publications

Egli A, Blanc DS, Greub G, Keller PM, Lazarevic V, Lebrand A, Leib S, Neher RA, Perreten V, Ramette A, Schrenzel J, Stephan R, Wagner K, Wuethrich D, Xenarios I. Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform. Swiss Med Wkly 2018;148:w14693

Wüthrich D, Blanc D, Greub G, Perreten V, Schrenzel J, Stephan R, Lebrand A, Xenarios I, Neher R, Egli A. Modern Microbiological Surveillance for Antibiotic Drug Resistance. In Federal Office of Public Health and Federal Food Safety and Veterinary Office. Swiss Antibiotic Resistance Report 2018. Usage of Antibiotics and Occurrence of Antibiotic Resistance in Bacteria from Humans and Animals in Switzerland, November 2018, FOPH publication number: 2018-OEG-87, 93-95.