About

Kaptive is a system for surface polysaccharide typing from bacterial genome sequences. It consists of two main components:

1. Curated reference databases of surface polysaccharide gene clusters (loci).
2. A command-line interface (CLI) with three modes:
   • assembly: surface polysaccharide typing from assemblies
   • extract: extract features from Kaptive databases in different formats
   • convert: convert Kaptive results to different formats

Kaptive can be found:

• On GitHub alongside the reference databases.
• On PathogenWatch where it is used to serotype Klebsiella and Acinetobacter baumannii isolates.
• As a GUI in Kaptive Web (source code), which includes a third-party database for Vibrio parahaemolyticus^1.

For full documentation, including install and usage instructions, click here.

Citation

• If you use Kaptive in your research, please cite^2.
• If you use the Klebsiella K or O locus databases, please cite^3 and^4.
• If you use Kaptive Web, please cite^5.
• If you use the A. baumannii K or OC locus database(s) in your research please cite^6 and^7.

Tutorial

Step-by-step video and documented tutorials are available, covering:

• Kaptive’s features and their scientific rationale
• How to run Kaptive
• Examples, illustrating how to run and interpret results
• Further investigations (e.g. exploring novel loci, IS insertions)

!!! note The tutorials are based on Kaptive 2.0, but the principles are similar for Kaptive 3.0.

People

• Dr. Tom Stanton
• A/Prof. Kelly L. Wyres
• Prof. Kathryn E. Holt
• Dr. Ryan R. Wick
• A/Prof. Johanna Kenyon

Contact Kelly and Tom for help with Kaptive, or to report bugs or request features.

References

A.L., 2023. Development of Kaptive databases for *Vibrio
parahaemolyticus* O- and K-antigen genotyping. *Microbial Genomics*
9. <https://doi.org/10.1099/mgen.0.001007>

Accurate in silico Antigen Typing with Kaptive 3.
2025 _Microbial Genomics_ 11(6):001428.
<https://doi.org/10.1099/mgen.0.001428>

Thomson, N.R., Holt, K.E., 2016. Identification of *Klebsiella*
capsule synthesis loci from whole genome data. *Microbial Genomics*
2, e000102. <https://doi.org/10.1099/mgen.0.000102>

2022. Kaptive 2.0: updated capsule and lipopolysaccharide locus
typing for the *Klebsiella pneumoniae* species complex. *Microbial
Genomics* 8. <https://doi.org/10.1099/mgen.0.000800>

User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for
*Klebsiella* Genomes. *Journal of Clinical Microbiology* 56,
10.1128/jcm.00197-18. <https://doi.org/10.1128/jcm.00197-18>

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* 6.
<https://doi.org/10.1099/mgen.0.000339>

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* 8.
<https://doi.org/10.1099/mgen.0.000878>