The Swiss Pathogen Surveillance Platform - towards a nation-wide One Health data exchange platform for bacterial, viral and fungal genomics and associated metadata

Abstract

The Swiss Pathogen Surveillance Platform (SPSP) is a shared secure surveillance platform between human and veterinary medicine, to also include environmental and foodborne isolates. It enables rapid and detailed transmission monitoring and outbreak surveillance of pathogens using whole genome sequencing data and associated metadata. It features controlled data access, complex dynamic queries, dedicated dashboards and automated data sharing with international repositories, providing actionable results for public health and the vision to improve societal well-being and health.

Keywords: antibiotic resistance; bacteria; bioinformatics; database; epidemiology; fungi; molecular surveillance; outbreaks; research; sequencing; typing; virulence; virus.

Fig. 1.

Map of institutions contributing data to SPSP. These partners have a data sharing agreement with SPSP. EB: executive board; SB: scientific board.

Fig. 2.

SPSP governance and ethical/legal framework. Representatives of the PARTIES constitute the Executive Board, which is the main decision body of SPSP. Upon request using the SPSP online form, new groups can ask to join SPSP as PARTIES (if interest in multiple pathogens) or as PARTNERS (if interest in a specific pathogen or project). PARTNERS are invited to join the Advisory Board. Experts from various institutions are invited to the Scientific Board. Access to sensitive data is carefully controlled with limited access to only minimal, non-sensitive data, by default, which can be extended to sensitive data upon acceptance by authorized bodies (ethics commissions, health authorities). Sensitive data may only be shared within secure IT infrastructures. Anonymized data are shared on public repositories to foster Open Data. CA: Consortium Agreement: DTUA: Data Transfer and Use Agreement.

Fig. 3.

SPSP architecture. SPSP is hosted on the SIB sensitive zone, which is the Lausanne BioMedIT node. The Vue.js web application is only accessible with two-factor authentication (managed with keycloak and SWITCH edu-ID, a secure Swiss digital identity) and for white-listed IP addresses. It communicates through dedicated APIs (application programming interface) with the Java backend that has access to the databases (DBs) and compute cluster (CPT). Developers and data curators can access the sensitive zone through a secure proxy server. Data are submitted to SPSP via the SPSP SFTP server, using the SPSP Transfer tool that encapsulates, compresses and GNU Privacy Guard (GPG)-encrypts every batch of data. Authentication on the SFTP server is managed by Secure SHell (ssh) keys and access is also controlled by IP whitelisting.

Fig. 4.

SPSP is a secure online platform for the analysis and sharing of One Health epidemiological and molecular data. 2FA: two-factor authentication. All icons from NounProject.com.

Fig. 5.

Switzerland’s contribution to global SARS-CoV-2 surveillance open data (top). Contribution by institution (bottom left). Contribution by country (bottom right). Graphs and table from COVID-19 Data Portal, as of October 2022, available at https://www.covid19dataportal.org/ and described in Harrison et al. [9].

Fig. 6.

Frontend screenshots of SPSP. Upper-left: project view with four samples and six fields (columns). Middle-right: creation of a new project with the query building tool. Bottom-left: plot from the SARS-CoV-2 dashboard illustrating submissions stratified by age category of patients.