EnteroBase joins ELIXIR-UK Services

EnteroBase has been added to the portfolio of endorsed ELIXIR-UK Services. Developed and maintained by the Bioinformatics & Digital Health Service at the University of Warwick, EnteroBase provides free access to tools and compute for bacterial pathogen genome assembly and analysis, hosting over 1.7 million curated bacterial genomes and metadata for a global community of more than 5,000 registered users in over 100 countries.

Standardising pathogen genomics across Europe

EnteroBase aligns with the Data, Compute and Tools Platforms, with additional relevance to Interoperability. It collects bacterial genome sequencing data and metadata from public sources including the European Nucleotide Archive (ENA), and allows users to submit read data directly into ENA via the NCBI Sequence Read Archive through a fully automated process. Its web-based tools cover genome assembly, annotation, genotyping (MLST, cgMLST, HierCC), phylogenetics and visualisation, requiring no local computational infrastructure and no user knowledge of bioinformatics.

Becoming an ELIXIR-UK Service recognises resources that are technically robust, well maintained and widely adopted across the UK life sciences community.

Sascha Ott, University of Warwick, said:

“Being recognised as an ELIXIR-UK Service reflects over a decade of development and strengthens EnteroBase’s connections to the European data infrastructure that underpins pathogen surveillance.”

National reach, global standardisation

EnteroBase is used daily by national reference laboratories including UKHSA and APHA, as well as international partners such as the Institut Pasteur and CICD, to characterise emerging pathogens. Coordinated but independent installations run at the Leibniz Institute DSMZ, in China, and are in development at UKHSA and in Gothenburg, adding resilience and allowing the platform to expand into further pathogens while supporting sites that handle sensitive data. A further instance, PhytoBacExplorer, is hosted in Warwick to serve the plant pathogen community, extending the EnteroBase model to support genomic surveillance and comparative analysis of important bacterial plant pathogens EnteroBase has been cited as a tool or data resource in at least 143 publications, and its 2020 User Guide has been cited more than 1,000 times in five years. A recent user survey recorded a Net Promoter Score of 61.

The University of Warwick has given a long-term commitment to host and maintain EnteroBase, and the platform was used as a Research Excellence Framework case study in the previous submission round. Future development will be supported through continued grant funding and an application for Global Core Biodata Resources status.