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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

Installation, usage and documentaton

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


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).

Related tools

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.