Focus on the group's mission
The Centre for Pathogen Bioinformatics, led by Eneida Hatcher, coordinates an integrated ecosystem of databases and tools for tracking and understanding infectious microbes through analysis of their genetic sequences (genomic surveillance).
These resources played major roles during the COVID-19 pandemic response and continue to underpin pathogen monitoring and research at the national and international level — from seasonal threats like SARS-CoV-2 and influenza to emerging ones like antibiotic-resistant bacteria and the recent Ebola and hantavirus outbreaks.
The Centre of Pathogen Bioinformatics is a cornerstone of public health — connecting the people who produce, use and govern pathogen data, and drawing out the signals that help faster responses to infectious diseases.
At the interface between public health and research, the Centre:
- offers expertise and services in pathogen bioinformatics, computational molecular epidemiology and related multi-site project management to Swiss Federal Authorities and within any Swiss endemic preparedness and molecular surveillance programme;
- ensures Switzerland remains at the forefront of data management and data analysis required for real-time surveillance;
- generates insights for evidence-based global pathogen response and public health strategies.
The Centre for Pathogen Bioinformatics provides expertise, resources and services to stakeholders across the data chain involved in pathogen surveillance, outbreak response and pandemic preparedness.
What is pathogen bioinformatics?
Pathogen bioinformatics is a field that combines principles and tools from bioinformatics to study and analyze pathogens—organisms that cause disease in their hosts, such as viruses, bacteria, fungi, and parasites.
This interdisciplinary field utilizes computational methods to understand the genetic and molecular mechanisms of pathogens, with the aim of improving disease diagnosis, treatment, prevention and outbreak monitoring.
Pathogen bioinformatics plays a crucial role in modern infectious disease research, offering insights that are essential for developing preventive and contingency measures by public authorities.
The Centre for Pathogen Bioinformatics strengthens SIB’s mission to generate knowledge and provide means for better health worldwide.
Supporting the needs of infectious disease stakeholders
Based on existing and new resources from SIB’s national network, the Centre for Pathogen Bioinformatics develops the following range of activities to support its many direct stakeholders and the entire research community in the field including notably:
What is pathogen bioinformatics?
Pathogen bioinformatics is a field that combines principles and tools from bioinformatics to study and analyze pathogens—organisms that cause disease in their hosts, such as viruses, bacteria, fungi, and parasites.
This interdisciplinary field utilizes computational methods to understand the genetic and molecular mechanisms of pathogens, with the aim of improving disease diagnosis, treatment, prevention and outbreak monitoring.
Pathogen bioinformatics plays a crucial role in modern infectious disease research, offering insights that are essential for developing preventive and contingency measures by public authorities.
The Centre for Pathogen Bioinformatics strengthens SIB’s mission to generate knowledge and provide means for better health worldwide.
Data hosting, management, processing, and sharing
The Centre offers services to data generators and data analysers for:
- central hosting and management of Swiss molecular data for pathogens of public health interest;
- provision of routine bioinformatics and digital automation support for reference laboratories, public health authorities and research laboratories;
- acting as data broker to international data repositories, for a large range of sample types isolated from patients, food, animals and the environment.
Developing open-source software based on the latest research:
- data-sharing infrastructure facilitating global exchange of FAIR (Findable, Accessible, Interoperable and Reusable) pathogen data;
- data-processing pipelines that include quality control and curation, as well as standard and specialized methods (typing, assembly, phylogenetics) supporting reproducible data analysis and open science principles.
Data analyses, interpretation & expert consultancy
- Collaboration with resources developed by SIB Groups in the field of pathogen bioinformatics and computational molecular epidemiology.
- Development of standardized descriptive statistical analyses and implementation of integrative dashboards and reports for public health authorities (e.g. pathogen data reports for the infectious disease dashboard of the Federal Office of Public Health), researchers and citizens in Switzerland and beyond.
- Provision of specialized analyses to support public health authorities.
- Development of new resources where gaps are identified.
International collaboration and alignment
- Active or leading role in international efforts for FAIR pathogen data access and sharing, including through the development of a global Pathogen Data Network.
- Harmonizing international data standards and practices, through the membership of Emma Hodcroft in the WHO International Pathogen Surveillance Network Community of Practice in Genomics Data.
- Alignment and collaboration with other international initiatives and infrastructures, including the ELIXIR Pathogen Data Focus Group, Global Microbial Identifier and Public Health Alliance for Genomic Epidemiology (PHA4GE).
Coordinating integrated tools for pathogen surveillance
Data analysis platforms and bioinformatics tools are crucial for enabling reproducible analysis of large and complex data sets. They also provide essential real-time surveillance information based on the combination of national and international data.
The Centre coordinates the following strategic resources developed or co-developed within SIB Groups in a sustainable, synergistic way — and in alignment with international initiatives to strengthen Switzerland’s role at the forefront of molecular surveillance and digital transformation.
Please refer to the individual resource websites to see more on their features, as well as their specific governance bodies and funding sources.
The Swiss Pathogen Surveillance Platform SPSP – 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 informs the FOPH's infectious disease dashboard and is a consortium whose members are listed here.
Nextclade - curation and annotation of datasets (Neher group, University of Basel & SIB, together with the group of Trevor Bedford)
Nextstrain - key surveillance tool during but also before the pandemic notably for Influenza where it supports yearly vaccine development (Neher group, University of Basel & SIB, together with the group of Trevor Bedford)
covSPECTRUM- SARS-CoV-2 dashboard for interactive querying of mutations and variants; it became a core tool for pango lineage designation proposals(Stadler group, ETHZ & SIB)
CoVariants - reference for the overview of variants and mutations (Hodcroft group, Swiss-TPH & SIB)
V-pipe - estimation of viral genomic diversity in clinical and environmental samples, including detection and quantification of genomic pathogen variants in wastewater and estimation of their relative fitness advantages (Beerenwinkel group, ETHZ & SIB)
Loculus - software package to power microbial genomic databases and Pathoplexus - open-source database supported by Loculus to enhance the sharing and analysis of human viral pathogen genomic data (Hodcroft, Neher & Stadler groups, STPH, UniBas, ETHZ & SIB)
Enhancing the sharing of pathogen data
The Centre’s projects build on strong collaborations forged over the years to further streamline data sharing from the local to the global level.
Pathogen Data Network (PDN). This international flagship project is working to enable a world-wide ecosystem of linked data and tools to support research and public health response to infectious diseases and major outbreaks. Now in its second year, PDN is leveraging SIB and US expertise and resources to provide accurate, fast and comprehensive insights into circulating and emerging pathogens. Funded by NIH-NIAID BRC programme. See news.
FAIRification of pathogen bioinformatics resources. The Centre’s ecosystem of resources was strengthened by increasing resource interoperability and providing an integrated system for analysis and sharing of pathogen genomic data. This work also supports genomic epidemiology globally. Funded by Swissuniversities B3.2 ORD Funding Scheme (FAIR-CPB project). See more.
Ensuring continued relevance through close research ties
The Centre for Pathogen Bioinformatics is governed by renowned Swiss and international experts in computational biology, pathogen evolution and epidemiology. This close connection with research ensures its activities keep pace with emerging pathogens as well as new understanding of pathogen biology, virulence, fitness and more.
Organization
Managing Director:
Eneida Hatcher
Steering Board:
Niko Beerenwinkel (Computational Biology)
Emma Hodcroft (EVE Epidemiology and Virus Evolution)
Richard Neher (Microbial Evolution)
Tanja Stadler (Computational Evolution)
Selected press coverage
Read the press release in German and French about the inauguration of the Centre in Bern, on 23 January 2025.
The launch of the Centre for Pathogen Bioinformatics was widely covered in the Swiss press, including:
- RTS – multimedia interviews with the Centre’s Managing Director, Aitana Neves, and SIB Executive Director Christophe Dessimoz (French)
- Le Temps – interview with Aitana Neves (French)
- 24 heures – interview with Aitana Neves and Christophe Dessimoz (French)
- La Liberté – interview with Aitana Neves (French)
- Tages Anzeiger – interview with Aitana Neves (German)
- Radio SRF 1 / Echo der Zeit – interview with Aitana Neves and Christophe Dessimoz (German)
