.. Kleborate documentation master file, created by sphinx-quickstart on Thu Apr 25 06:02:56 2024. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. .. toctree:: :maxdepth: 1 :hidden: Installation Usage modules Creating-New-Modules ######################## Introducing Kleborate v3 ######################## Kleborate was primarily developed to screen genome assemblies of *Klebsiella pneumoniae* and the *Klebsiella pneumoniae* species complex (KpSC) for: * Species (e.g. *K. pneumoniae*\ , *K. quasipneumoniae*\ , *K. variicola*\ , etc.) * *K. pneumoniae* MLST sequence type * *ICEKp* associated virulence loci: yersiniabactin (*ybt*), colibactin (*clb*), salmochelin (*iro*), hypermucoidy (*rmpA*) * Virulence plasmid associated loci: salmochelin (\ *iro*\ ), aerobactin (\ *iuc*\ ), hypermucoidy (\ *rmpA*\ , *rmpA2*\ ) * Antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases * K (capsule) and O antigen (LPS) serotype prediction, via *wzi* alleles and `Kaptive `_ `Kleborate v3 `_ includes a rewrite of the code to (i) replace the use of BLAST with minimap (faster and less buggy); and (ii) introduce a modular structure making it easy to add new typing modules, including for other species. For *K. pneumoniae* species complex, **Kleborate v3 can reproduce the outputs of Kleborate v2 by running the preset modules for KpSC via:** .. code-block:: Python kleborate -a *.fasta -o kleborate_results -p kpsc --trim_headers (Note the command has changed from Kleborate v2, the above is equivalent to running ``kleborate --all -o results.txt -a *.fasta`` with Kleborate v2 and includes all resistance and Kaptive-based typing) **New modules for other species are in development,** for now these include MLST schemes for *Klebsiella oxytoca* species complex and *Escherichia coli* (see the Modules page). Citations ---------- If you use Kleborate, please cite the paper: Lam, MMC. et al. A genomic surveillance framework and genotyping tool for *Klebsiella pneumoniae* and its related species complex, *Nature Communications* (2021). ``_ If you use the Kaptive calls for K and O locus typing please also cite Wyres, KL. et al. Identification of *Klebsiella* capsule synthesis loci from whole genome data. *Microbial Genomics* (2016). ``_ The following papers provide more information on the component schemes and genotyping incorporated in Kleborate: .. Yersiniabactin and colibactin (*ICEKp*): Lam, MMC. et al. Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element *ICEKp* in *Klebsiella pneumoniae* populations. *Microbial Genomics* (2018). `Microbial Genomics `_ Aerobactin and salmochelin: Lam, MMC. et al. Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in *Klebsiella pneumoniae*. *Genome Medicine* (2018). `Genome Medicine `_ Kaptive for capsule (K) serotyping: Wyres, KL. et al. Identification of *Klebsiella* capsule synthesis loci from whole genome data. *Microbial Genomics* (2016). `Microbial Genomics 2 `_ Kaptive for O antigen (LPS) serotyping: Wick, RR et. al. Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction for *Klebsiella* genomes. *Journal of Clinical Microbiology* (2018). `Journal of Clinical Microbiology `_ Changes from v2 ---------------- When Kleborate v3 is run using the ``-p kpsc`` option to run preset modules for *K. pneumoniae* the same logic is implemented as Kleborate v2, plus the following changes/updates: * MLST & virulence databases updated (April 2024) * Column ``Chr_ST`` has been removed in v3, as it is redundant with ``ST`` * AMR database updated based on CARD v3.2.9 (June 2024) * Added ``$`` to indicate when PmrB or MgrB have a mutation in the start codon that may disrupt translation (in ``Col_mutations`` column) * Added check for synonymous mutation in ompK36 (25 C > T) associated with increased resistance to carbapenems (in ``Omp_mutations`` column) * Updated to use Kaptive v3, which has some changes to the names of output variables: * ``K_locus_missing_genes`` has been renamed ``K_Missing_expected_genes`` * ``O_locus_missing_genes`` has been renamed ``O_Missing_expected_genes`` * Added new AMR genotyping report compatible with the `hAMRonization `_. standard developed by the Public Health Alliance for Genomic Epidemiology (PHA4GE). * Added a module for Ciprofloxacin resistance prediction * Mutations are reported using `HGVS nomenclature `_. * Added new modules for *Escherichia* species: pathotyping, typing of the LEE pathogenicity island, ClermonTyping, typing of stx types using StxTyper, O:H serotyping using ECTyper, AMR typing using AMRFinderPlus Tutorial -------- A step-by-step tutorial for Kleborate v3 is available at `kleborate-workshop `_, covering: * Kleborate's features and their scientific rationale * How to run Kleborate * Examples, illustrating how to run and interpret results Public reports ---------------- The `Kleborate paper `_ reports results of genotyping ~10,000 public genomes that have been filtered to remove redundant sequences (e.g. outbreak clusters, identified as small genome-wide mash distance with same year, location and genotypes), with Kleborate v2. The results can be explored in `Microreact `_ (which shows the mash tree, Kleborate output & curated metadata) or `Kleborate-Viz `_ (R shiny app). Kleborate-Viz also has the EuSCAPE dataset preloaded, or you can view your own Kleborate results. Kleborate is also included in `Klebsiella Pathogenwatch `_ which shows interactive trees, maps and line lists for *Klebsiella pneumoniae* and allows you to analyse your own data in context of the public collections. See `this paper `_ for an example of how to use it. Contact us ---------- Kleborate is under active development with many other Klebs genomic analysis tools and projects in progress (see `github.com/klebgenomics `_). Please get in touch via the GitHub `issues tracker `_ if you have any issues, questions or ideas. For more on our lab, including other software, see `http://holtlab.net `_ License ------- `GNU General Public License, version 3 `_