PubMLST: Disseminating and exploiting bacterial diversity data for public health benefit (360G-Wellcome-218205_Z_19_Z)

Multilocus sequence typing (MLST) has been the principal approach to bacterial strain characterization for > 20 years and is increasingly employed for whole genome sequence (WGS) analyses (whole genome and core-genome MLST). PubMLST (https://pubmlst.org) provides a major international resource for the storage, analysis, and dissemination of assembled microbial WGS data and hosts > 100 databases that provide MLST nomenclature and link curated genetic, provenance, phenotype, and population data. The PubMLST resource, which has existed in various guises since 1998, operates from an Oxford-based web server and uses the open-source and open-access software platform BIGSdb, which was specifically developed for this purpose. PubMLST provides services to a wide variety of other resources, some of which employ the BIGSdb software. PubMLST also hosts the ribosomal MLST (rMLST) database, which enables bacterial species identification by cross-referencing > 1.5M ribosomal allele sequences to a validated dataset of ~250,000 genomes representing 9500 bacterial species. Ongoing development of BIGSdb facilitates complex data querying and comparative analyses through a web interface. Data can also be retrieved and queried by other external (e.g. public health) databases via a programming interface. This application seeks to continue the operation and development of PubMLST, specifically enhancing the reuse of data is a major goal.