Kleborate
Klebsiella comprehensive AMR and typing analysis software.
About Kleborate
For a detailed explanation about the Kleborate tool and outputs in general, please view their documentation at: https://kleborate.readthedocs.io/en/latest/index.html.
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 Profiles
K. pneumoniae species complex
Genomes determined to members of the K. pneumoniae species complex are searched using the -p kpsc flag.
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.
K. oxytoca species complex
Genomes determined to members of the K. pneumoniae species complex are searched using the -p kpsc flag.
The Kleborate output splits into two main sections:
Typing - Species/MLST and other typing outputs.
Virulence Locus Typing - Allele and ST codes for virulence loci.
Other Klebsiella genus
Genomes determined to be of other species Klebsiella are seached using the -m enterobacterales__species flag. This allows confirmation of the species assignment. Any discrepency is reported in the Genome Report
The Kleborate species assignment module is run in all cases. If there is a difference in the assignment this is reported in red at the top of the Genome Report. This difference can be due to how recently the respective species assignment tools have been updated, which can include updates in species definitions or corrections to the reference genome assignments. It can also be indicative of a contaminated or low quality genome .
Typing
Species
The assigned species according to Kleborate. This can conflict with the output of Speciator, and is more likely to be correct.
Virulence Score
Virulence scores (0-5) 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.
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://kleborate.readthedocs.io/en/latest/index.html. 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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