kleborate 3.2.4

Kleborate: a tool for typing and screening pathogen genome assemblies

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://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