Kleborate

Klebsiella comprehensive AMR and typing analysis software.

About Kleborate

Current Kleborate version: v2.2.0.

For a detailed explanation about the Kleborate tool and outputs in general, please view their documentation at: http://bit.ly/kleborate-workshop.

The Kleborate software from Holt et al provides in depth species, ST, virulence genes, capsule typing and antimicrobial resistance prediction for Klebsiella. Results are displayed in the Genome Report and in the "Typing" table of the Collection View, and can be downloaded from both download menus.

Kleborate is focussed on the Klebsiella pneumoniae complex (KpSC). Typing and inexact virulence locus results for Klebsiella species outside of this complex should be treated with care.

The Kleborate output splits into four main sections:

  1. Typing - Species/MLST and other typing outputs.

  2. Virulence Locus Typing - Allele and ST codes for virulence loci.

  3. Predicted AMR - AMR genes and alleles grouped by resistance phenotype.

  4. Beta-Lactamase Genes By Class - BLA genes grouped by Lahey classes.

Each section is described below with links to the source documentation from Kleborate.

Typing

Species

The assigned species according to Kleborate. This can conflict with the output of Speciator, and is more likely to be correct.

Virulence/Resistance Score

Virulence (0-5) and resistance scores (0-3) determined by Kleborate.

K/O Locus

The K and O locus names and confidence in the assignments as determined by Kaptive. For references see below.

The following virulence loci and types are determined by Kleborate:

  • Yersiniabactin/YbST

  • Colibactin/CbST

  • Aerobactin/AbST

  • Salmochelin/SmST

  • RmpA, RmpA2 (hypermucoidy)

Kleborate AMR profiles and determinants are displayed in the genome reports and collection views. The following antimicrobials are classified by Kleborate.

Kleborate columnPathogenwatch Antimicrobial Name

AGly_acquired

Aminoglycosides

Col_acquired

Colistin

Col_mutations

Colistin

Fcyn_acquired

Fosfomycin

Flq_acquired

Fluoroquinolones

Flq_mutations

Fluoroquinolones

Gly_acquired

Glycopeptides

MLS_acquired

Macrolides

Phe_acquired

Phenicols

Rif_acquired

Rifampicin

Sul_acquired

Sulfonamides

Tet_acquired

Tetracycline

Tgc_acquired

Tigecycline

Tmt_acquired

Trimethoprim

Bla_chr

Beta-Lactams

Bla_mutations

Beta-Lactams

Bla_inhR_acquired

Beta-lactams+Inhibitors

Bla_ESBL_acquired

ESBLs

Bla_ESBL_acquired_inhR

ESBLs+Inhibitors

Bla_Carb_acquired

Carbapenems

SHV

Other

Omp

OmpK35/OmpK36

Citing Kleborate

For a detailed description of the Kleborate and its output, we recommend visiting https://github.com/katholt/Kleborate/wiki. If you use the results of Kleborate in your publications or on the web please cite the version (provided in the CSV file download or at the top of this page) and the Kleborate publication. If you use the Kaptive K/O antigen assignments, please also cite the associated paper(s).

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