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Kleborate

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: acquired genes, SNPs, gene truncations and intrinsic β-lactamases
  • K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive

For full documentation, please go to the Kleborate wiki!

If you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).

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

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