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:

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.

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:

1. Typing - Species/MLST and other typing outputs.
2. 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 .

An example of where Kleborate has assigned a different species to Pathogenwatch

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.

Virulence Locus Typing

The following virulence loci and types are determined by Kleborate:

• Yersiniabactin/YbST

• Colibactin/CbST

• Aerobactin/AbST

• Salmochelin/SmST

• RmpA, RmpA2 (hypermucoidy)

Inferred Antimicrobial Resistance

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://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).

• Kleborate: Lam et al. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nature Communications (2021).