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.
