Kleborate was primarily developed to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:
- Species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.)
- K. pneumoniae species complex MLST
- ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmp)
- Virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmp, 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
Kleborate v3 includes a rewrite of the code to (i) replace the use of BLAST with minimap2 (faster and less buggy); and (ii) introduce a modular structure making it easy to add new typing modules, including for other species. Currently, functionality for other species is limited to MLST for Klebsiella oxytoca species complex and Escherichia coli but more is in development.
A list of changes from v2 is available in the documentation.
Documentation
For information on how to install and run Kleborate v3, please visit the Docs.
Citation
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). https://doi.org/10.1038/s41467-021-24448-3
If you use the Kaptive calls for K and O locus typing please cite: Stanton et al. Fast and accurate in silico antigen typing with Kaptive 3. Microbial Genomics (2025). https://doi.org/10.1099/mgen.0.000102
If you use the cgMLST and LIN code calls, please cite the paper: Bogaerts et al. MiST: rapid, accurate and flexible (core-genome) multi-locus sequence typing (MLST) allele calling from draft genomes. BMC Genomics (2025). https://doi.org/10.1186/s12864-025-12324-z
For a full list of acknowledgments and citations for third-party tools and databases used by Kleborate, please see the Docs.