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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. 1.
    ​Typing - Species/MLST and other typing outputs.
  2. 2.
    ​Virulence Locus Typing - Allele and ST codes for virulence loci.
  3. 3.
    ​Predicted AMR - AMR genes and alleles grouped by resistance phenotype.
  4. 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 column
Pathogenwatch 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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Last modified 4mo ago