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:
Typing - Species/MLST and other typing outputs.
Virulence Locus Typing - Allele and ST codes for virulence loci.
Predicted AMR - AMR genes and alleles grouped by resistance phenotype.
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 |
How to cite
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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