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Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:

• MLST sequence type
• species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.)
• ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)
• virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)
• antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases
• K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive

All the info you need to install Kleborate, run it, and interpret results is in the Kleborate wiki!

A step-by-step tutorial, illustrating how to use Kleborate and interpret the data, is available at bit.ly/kleborate-workshop

If you use Kleborate, please cite the paper: Lam, MMC. et al. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nature Communications (2021).

If you turn on the Kaptive option for full K and O typing, please also cite Kaptive directly: Identification of Klebsiella capsule synthesis loci from whole genome data. Microbial Genomics (2016).

You may also be interested in Kleborate-viz, a ShinyR app for visualising Kleborate output.

Users not comfortable runnnig Kleborate locally via the commandline may like to try uploading your genomes (reads or assemblies) to the drag-and-drop genomic epi online platform PathogenWatch - all genomes identified as Klebsiella pneumoniae will automatically be passed to Kleborate and Kaptive to generate a genotyping report, which can be downloaded in tabular format compatible with Kleborate-viz. See this paper for more about Klebsiella Pathogenwatch.