Kaptive is a tool for bacterial surface polysaccharide locus typing and variant evaluation. It takes one or more pre-assembled genomes and for each finds the best matching locus from a reference database. References for Klebsiella pneumoniae species complex and Acinetobacter baumannii are available in Kaptive's web interface.
The reference databases are curated by Kelly Wyres (Monash University, Australia) and Johanna Kenyon (Queensland University of Technology, Australia). Please contact us if you have an intact novel locus that you would like to be included.
If you use Kaptive's web interface please cite the paper below along with the reference for the relevant locus database(s).
Wick RR, Heinz E, Holt KE and Wyres KL 2018.
Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction for Klebsiella genomes. Journal of Clinical Microbiology: 56(6). e00197-18
K. pneumoniae species complex capsule (K) locus database
Wyres KL, Wick RR, Gorrie C, Jenney A, Follador R, Thompson N and Holt KE 2016.
Identification of Klebsiella capsule synthesis loci from whole genome data. Microbial Genomics doi: https://doi.org/10.1099/mgen.0.000102
K. pneumoniae species complex LPS (O) locus database
Lam MMC, Wick RR, Judd LM, Holt KE and Wyres KL 2022.
Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex. Microbial Genomics doi: https://doi.org/10.1099/mgen.0.000800
A. baumannii capsule (K) locus database
Cahill SM, Hall RM and Kenyon JJ 2022.
An update to the database for Acinetobacter baumannii capsular polysaccharide locus typing extends the extensive and diverse repertoire of genes found at and outside the K locus. bioRxiv doi: https://doi.org/10.1101/2022.05.19.492579
A. baumannii LPS (OC) locus database
Wyres KL, Cahill SM, Holt KE, Hall RM and Kenyon JJ 2020.
Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive. Microbial Genomics doi: 10.1099/mgen.0.000339
A full list of citations for the individual A. baumannii K- and OC- locus reference sequences can be found here.
V. parahaemolyticus capsule (K) and LPS (O) locus databases
van der Graaf–van Bloois L, Chen H, Wagenaar JA, Zomer AL 2022.
Development of Kaptive databases for Vibrio parahaemolyticus O- and K-antigen serotyping. bioRxiv doi: https://doi.org/10.1101/2021.07.06.451262
Current database version (as of 5th October 2022): Kaptive v2.0.4
Get Started |
Kaptive team |
Kaptive on GitHub |
Kaptive is an open source project for the biomedical community, licensed under GNU General Public License version 3. |
Kaptive is developed and maintained by Kelly Wyres, Ryan Wick, Tom Stanton and Kathryn Holt at the Holt Lab, Monash University. |
The command line version of Kaptive can be deployed on your computer with Klebsiella or A. baumannii K-locus, O/OC-locus or other databases. |
| Submit job | Visit Holt lab | Visit GitHub |