# Kleborate ## About Kleborate {% hint style="info" %} For a detailed explanation about the Kleborate tool and outputs in general, please view their documentation at: . {% endhint %} The [Kleborate software from Holt et al](https://github.com/katholt/Kleborate) provides in depth species, ST, virulence genes, capsule typing and antimicrobial resistance prediction for Klebsiella. Results are displayed in the [Genome Report](/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/browsing-searching-genomes.md#genome-reports) and in the "Typing" table of the [Collection View,](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv.md) 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](#typing) - Species/MLST and other typing outputs. 2. [Virulence Locus Typing](#virulence-locus-typing) - Allele and ST codes for virulence loci. 3. [Predicted AMR ](#predicted-amr)- AMR genes and alleles grouped by resistance phenotype. 4. [Beta-Lactamase Genes By Class](#beta-lactamase-genes-by-class) - BLA genes grouped by [Lahey](https://www.lahey.org/Studies/) classes. Each section is described below with links to the source documentation from [Kleborate](https://github.com/katholt/Kleborate#table-of-contents). #### 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](#typing) - Species/MLST and other typing outputs. 2. [Virulence Locus Typing](#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](/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/genome-reports.md) {% hint style="warning" %} 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 . {% endhint %}

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

### Typing #### Species The assigned species according to [Kleborate](https://github.com/katholt/Kleborate#klebsiella-species). This can conflict with the output of [Speciator](/pathogenwatch/technical-descriptions-of-analysis-tools/speciator.md), and is more likely to be correct. #### Virulence Score Virulence scores (0-5) determined by [Kleborate](https://github.com/katholt/Kleborate#scores-and-counts). #### K/O Locus The K and O locus names and confidence in the assignments as determined by [Kaptive](https://github.com/katholt/Kaptive). For references see [below](#citing-kleborate). ### [Virulence Locus Typing](https://github.com/katholt/Kleborate#virulence-loci) The following virulence loci and types are determined by [Kleborate](https://github.com/katholt/Kleborate#virulence-loci): * Yersiniabactin/YbST * Colibactin/CbST * Aerobactin/AbST * Salmochelin/SmST * RmpA, RmpA2 (hypermucoidy) ### [Inferred Antimicrobial Resistance](https://github.com/katholt/Kleborate#resistance-gene-detection) 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 . 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](https://github.com/katholt/kaptive), 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)*](https://www.nature.com/articles/s41467-021-24448-3)*.* --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/kleborate.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.