SPSP in a nutshell

The Swiss Pathogen Surveillance Platform (SPSP) is a secure One-health online platform that enables near real-time sharing under controlled access of pathogen sequencing data and their associated clinical/epidemiological metadata.

SPSP overview

Metadata are structured using existing ontologies (SNOMED CT, NCBI Taxonomy) and controlled vocabularies whenever possible. WGS are then analyzed using harmonized bioinformatics methods for quality control, assembly, typing and outbreak analyses.

The SPSP online portal is hosted at SIB Swiss Institute of Bioinformatics and complies with the Swiss Personalized Health Network (SPHN) data security standards and in particular with the SPHN Information Security Policy (ISP), notably including encrypted transfer and storage of data, and dual-factor authentication.

Purpose and aim

SPSP serves two main objectives:

  • SURVEILLANCE: serve as a shared surveillance platform between human and veterinary medicine, including environmental and food isolates in the near future, thereby enabling detailed transmission and outbreak surveillance of pathogens in near real-time, with actionable results for public health. May require access to personal data, as regulated by the Federal Law and Ordinance on Epidemics (LEp).
  • RESEARCH: serve as a repository of structured, standardized and well-annotated data that can be used to answer specific research questions. May require access to personal data, as regulated by the Human Research Act and Ordinance on Human Research.

To achieve these goals, SPSP acts as a central repository securely hosting WGS data and their associated metadata, which are made accessible to registered users under strict rules following the above-mentioned regulations, and as described in „Data use and access“.

Envisioned benefits:

  • Identify risks of MDR bacterial pathogens for hospitals and public health in Switzerland and other European countries.
  • Describe and explore these risks by predicting dynamics of spread.
  • Serve as outcome control measurements of interventions e.g. by monitoring the reduction of particular clones.

Funding and Support

The Swiss Pathogen Surveillance Platform has received funding from the following bodies:

In addition, the University Hospital of Basel and the SIB Swiss Institute of Bioinformatics have provided additional resources for the development of SPSP. Please get in touch with us (aegli@imm.uzh.ch, aitana.neves@sib.swiss) if you wish to support our initiative.


Neves A, Walther D, Martin-Campos T, Barbie V, Bertelli C, Blanc D, Bouchet G, Erard F, Greub G, Hirsch HH, Huber M, Kaiser L, Leib SL, Leuzinger K, Lazarevic V, Mäusezahl M, Molina J, Neher RA, Perreten V, Ramette A, Roloff T, Schrenzel J, Seth-Smith HMB, Stephan R, Terumalai D, Wegner F, Egli A. The Swiss Pathogen Surveillance Platform – towards a nation-wide One Health data exchange platform for bacterial, viral and fungal genomics and associated metadata. Microb Genom. 2023 May;9(5). doi: 10.1099/mgen.0.001001. PMID: 37171846.

Egli A, Blanc DS, Greub G, Keller PM, Lazarevic V, Neves 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.

Wüthrich D, Blanc D, Greub G, Perreten V, Schrenzel J, Stephan R, Neves 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.