Kaptive is a tool for bacterial in silico serotyping. 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, Acinetobacter baumannii and Vibrio parahaemolyticus 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.
The third-party database for Vibrio parahaemolyticus is maintained by Aldert Zomer.
The current versions are: Kaptive Web v1.3.0 and Kaptive v3.0.0b6. The individual database versions are shown in the citations section.
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
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
Current database version (as at 14 November 2022): v2.0.4
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
Current database version (as at 14 November 2022): v2.0.4
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. Microbial Genomics doi: https://doi.org/10.1099/mgen.0.000878
Current database version (as at 14 November 2022): v2.0.4
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
Current database version (as at 14 November 2022): v2.0.4
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 at 14 November 2022): v0.0.1
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 Tom Stanton and Kelly Wyres at the Wyres 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 Wyres lab | Visit GitHub |