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 MLST sequence type
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
Kleborate v3 includes a rewrite of the code to (i) replace the use of BLAST with minimap (faster and less buggy); and (ii) introduce a modular structure making it easy to add new typing modules, including for other species.
For K. pneumoniae species complex, Kleborate v3 can reproduce the outputs of Kleborate v2 by running the preset modules for KpSC via:
kleborate -a *.fasta -o kleborate_results -p kpsc --trim_headers
(Note the command has changed from Kleborate v2, the above is equivalent to running kleborate --all -o results.txt -a *.fasta with Kleborate v2 and includes all resistance and Kaptive-based typing)
New modules for other species are in development, for now these include MLST schemes for Klebsiella oxytoca species complex and Escherichia coli (see the Modules page).
Citations#
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://www.nature.com/articles/s41467-021-24448-3
If you use the Kaptive calls for K and O locus typing please also cite Wyres, KL. et al. Identification of Klebsiella capsule synthesis loci from whole genome data. Microbial Genomics (2016). http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000102
The following papers provide more information on the component schemes and genotyping incorporated in Kleborate:
Yersiniabactin and colibactin (ICEKp):Lam, MMC. et al. Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations. Microbial Genomics (2018). Microbial Genomics
Aerobactin and salmochelin:Lam, MMC. et al. Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae. Genome Medicine (2018). Genome Medicine
Kaptive for capsule (K) serotyping:Wyres, KL. et al. Identification of Klebsiella capsule synthesis loci from whole genome data. Microbial Genomics (2016). Microbial Genomics 2
Kaptive for O antigen (LPS) serotyping:Wick, RR et. al. Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction for Klebsiella genomes. Journal of Clinical Microbiology (2018). Journal of Clinical Microbiology
Changes from v2#
When Kleborate v3 is run using the -p kpsc option to run preset modules for K. pneumoniae the same logic is implemented as Kleborate v2, plus the following changes/updates:
MLST & virulence databases updated (April 2024)
Column
Chr_SThas been removed in v3, as it is redundant withSTAMR database updated based on CARD v3.2.9 (June 2024)
Added
$to indicate when PmrB or MgrB have a mutation in the start codon that may disrupt translation (inCol_mutationscolumn)Added check for synonymous mutation in ompK36 (25 C > T) associated with increased resistance to carbapenems (in
Omp_mutationscolumn)Updated to use Kaptive v3, which has some changes to the names of output variables:*
K_locus_missing_geneshas been renamedK_Missing_expected_genes*O_locus_missing_geneshas been renamedO_Missing_expected_genes* New columns are included in Kleborate v3:K_Coverage,O_Coverage
Tutorial#
A step-by-step tutorial for Kleborate v2 is available at kleborate-workshop, covering:
Kleborate’s features and their scientific rationale
How to run Kleborate
Examples, illustrating how to run and interpret results
How to visualise results using Kleborate-Viz
Performance of Kleborate on nanopore data
This tutorial will be updated soon to Kleborate v3, however the functionality of Kleborate v3 remains the same if you add -preset kpsc to the run command.
Public reports#
The Kleborate paper reports results of genotyping ~10,000 public genomes that have been filtered to remove redundant sequences (e.g. outbreak clusters, identified as small genome-wide mash distance with same year, location and genotypes), with Kleborate v2. The results can be explored in Microreact (which shows the mash tree, Kleborate output & curated metadata) or Kleborate-Viz (R shiny app). Kleborate-Viz also has the EuSCAPE dataset preloaded, or you can view your own Kleborate results.
Kleborate is also included in Klebsiella Pathogenwatch which shows interactive trees, maps and line lists for Klebsiella pneumoniae and allows you to analyse your own data in context of the public collections. See this paper for an example of how to use it.
Contact us#
Kleborate is under active development with many other Klebs genomic analysis tools and projects in progress (see github.com/klebgenomics).
Please get in touch via the GitHub issues tracker if you have any issues, questions or ideas.
For more on our lab, including other software, see http://holtlab.net
