The BIGSdb-Pasteur web platform is an integrated resource for genomic-based strain taxonomy, offering reference nomenclature databases, genomic libraries and comparative genomics tools. The platform is powered by the Bacterial Isolate Genome Sequence database software (Oxford University).
BIGSdb-Pasteur hosts a collection of curated multilocus sequence typing (MLST), whole-genome based typing (core genome cgMLST) and supplementary schemes (antimicrobial resistance, virulence, ...) for bacterial pathogens of public health importance, including Klebsiella pneumoniae and Listeria monocytogenes. Contextual, genomics and typing data of thousands of bacterial isolates are also accessible and queryable through the website. Please see our usage policy for commercial or large-scale usage of the data.
BIGSdb-Pasteur combines open databases and stable bioinformatics solutions that allow mining the sequences of bacterial isolates to define their genotype, sublineage, antimicrobial resistance genes, and pathogenic features, while maintaining a common nomenclature. Single- or multiple-user projects can be created from the web interface to facilitate the analysis of stored data and/or data upload. Although BIGSdb-Pasteur follows the philosophy of open data, uploading data through private projects is also supported to ensure the privacy of sensitive data, pending original publications and patent developments. Each species database in BIGSdb-Pasteur represents a resource providing the worldwide community with the collection, analysis and visualization of bacterial pathogenic strains. An application programming interface (API) allows the interaction of the database with analytical pipelines and third-party applications with graphical interfaces to facilitate users in the interpretation of results.
BIGSdb-Pasteur is constantly evolving and rapidly expanding both in terms of data content, as several experts are dedicated to database curation, and thousands of users continue to contribute by submitting genomic data corresponding to known or newly emerging bacterial genotypes.