Pasteur and Oxford Join Forces for a Sustainable Platform of Microbial Strain Classification

A central resource for public health microbiology

Antimicrobial-resistant bacterial infections affect millions of lives worldwide. Understanding how pathogenic agents evolve and spread across geographies and hosts is crucial for outbreak response and epidemiological surveillance. For more than 25 years, the Institut Pasteur and the University of Oxford have worked together to maintain a microbial genomic platform (BIGSdb) that allows disease surveillance, outbreak tracking, and research on antimicrobial resistance (AMR).

This innovative tool, which is used internationally by scientists, public health networks, infection control professionals and policymakers in multiple sectors including human and veterinary medicine and food industry, helps us understand and track the bacteria and viruses that cause some of the most serious diseases . The platform gathers essential genomic information and allows the use of a common “language” for the classification, naming, identification and comparison of different strains of bacteria and other pathogens, including those responsible for notorious diseases such as meningitis, pneumonia, and foodborne infections.

At its core, this platform acts as a global library of genetic information. It collects and organises the DNA of disease-causing pathogens for quick identification and comparison of different strains. This is crucial for recognising how outbreaks start, how they spread, and how we can stop them.

The platform is based on the BIGSdb application, developed by the University of Oxford, and includes many pathogen-specific databases divided between Institut Pasteur (https://bigsdb.pasteur.fr/) and the University of Oxford (https://pubmlst.org/).

Professor Martin Maiden

Head of The Department of Biology
University of Oxford

“Global problems need global solutions, and global research needs a sustainable common global language. In 1998 the development of MLST at Oxford provided such a language for bacterial typing, which has been widely adopted. The LIN code system, pioneered and first implemented at the Institute Pasteur in 2022, takes this approach to genomic levels of resolution.”

Impact of the platform on global health

The microbial genomic resources hosted in the BIGSdb platform allow users to classify and track the genetic variants of bacteria and other pathogens. Understanding the genetic makeup of bacteria and viruses allow scientists to:

Track how diseases change over time and in different world regions and sectors, using a One Health approach.
Respond faster and more effectively to outbreaks through the rapid identification of bacterial strains responsible for an epidemic.
Spot resistance to antibiotics or vaccines in specific geographies through the identification of antimicrobial resistant genes and emerging strains.
Design better treatments and vaccines through monitoring how well vaccines protect against different strains, according to world regions and time.

The platform is already supporting local healthcare teams in countries across the global south and beyond to take control of disease management in their own communities. By providing accesible, up-to-date genetic information, the platform helps local healthcare workers to:

See which pathogens are spreading in their regions.
Understand which vaccines or treatments are working, and where they aren't.
Use the data to influence policy making and adapt national and regional health strategies based on real-time evidence.

This kind of molecular data is vital for shaping vaccine policy, improving how we use antibiotics and antivirals, and ensuring resources go where they are most needed.

Finally, the platform is designed not just to deliver information, but to build long-term capacity in the regions that need it most. This means:

Creating local infrastructure for collecting and analysing data through networks like the Pasteur Network.
Offering training programmes at a variety of different levels - from school students to healthcare workers and policymakers to understand how to use the resource.
Helping communities understand why vaccination matters and how to use it most effectively.
Empowering people to make evidence-based decisions in their own healthcare systems.

Professor Sylvain Brisse

Director, Biodiversity and Epidemiology of Bacterial Pathogens Unit
Institut Pasteur

“The partnership between the University of Oxford and the Institut Pasteur achieves a broad coverage of bacterial infections and world regions under scrutiny by joining our complementary expertise in pathogenic agents and range of countries where diseases are under surveillance, and providing training for researchers and healthcare professionals.”

Why Pasteur and Oxford?

Initially developed seperately, covering different pathogens dependent on the expertise of the researchers in place, the Pasteur and Oxford teams are now working to integrate their world-leading genomic databases. Combined, these databases hold the genetic blueprints of virtually all major pathogens causing disease in humans, making it the most comprahensive resource of its kind.

The unified resource allows researchers to identifiy new targets for vaccines and treatments, understand how pathogens are evolving on a global scale and detect where resistance is developing in populations.

Another unique strength of this partnership is its billingual approach. Thanks to the collaboration between French-speaking Institut Pasteur and English-speaking University of Oxford, training materials and tools are available in both French and English. This is especially important in many African countries, where either French or English is often the primary language. This billingual approach ensures that more people can use the platform, understand the data and apply the insights to protect their communities.

The tool is invaluable for finding new ways to fight disease, grounded in data, powered by science and made accessible for all.

Sustaining a Global Resource

Both Institut Pasteur and the University of Oxford are committed to maintain the platform data freely accessible for public health purposes, in line with the FAIR principles (Findable, Accessible, Interoperable, and Reusable).

As data volumes grow and the demand for curated data increases, sustaining the many databases requires significant human and financial investment. To secure the future of this platform, IP and OU are willing to develop a sustainable funding model, where open access to the databases will continue for academic and public health usage.

The partners are also working to expand the platform’s functionalities, improve data quality control, implement new tools, improve the reliability and interoperability of the platform with other resources, and develop training programs for researchers and healthcare professionals.

Programme Directors

The programme is jointly led by representatives from the Institut Pasteur and the University of Oxford. These are:

Professor Sylvain Brisse Director, Biodiversity and Epidemiology of Bacterial Pathogens Unit at Institut Pasteur
Professor Martin Maiden Head of the Department of Biology at the University of Oxford
Dr Solène Cottis Department of Global Health at Institut Pasteur
Dr Keith Jolley Bioinformatician at the University of Oxford

How can you help?

The Pasteur-Oxford platform recent achievements illustrate how collaborative efforts between these two outstanding institutions can improve global public health. Its continued success depends on philanthropic support to ensure it remains a global common good.

Every donation helps us maintain and expand the platform. Your support will make a difference in public health by advancing standardisation in the genomic epidemiology of pathogenic agents, improving knowledge on antimicrobial resistance emergence and how vaccines can help to control this pressing public health issue. The platform enhances knowledge on infectious agents, strengthens global collaboration, and improves globally coordinated surveillance and outbreak responses.

If you would like to learn more about how you can support this project, please get in touch at info@pasteurfoundation.uk

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