Introducing Kaptive 3

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 [3].

Citation

• If you use Kaptive and the Klebsiella K or O locus databases in your research, please cite [6] and [2].

• If you use Kaptive Web, please cite [4].

• If you use the A. baumannii K or OC locus database(s) in your research please cite [5] and [1].

• Lists of papers describing each of the individual A. baumannii reference loci can be found here.

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

• Dr. 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

[1]

Cahill, S.M., Hall, R.M., Kenyon, J.J., 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 8. https://doi.org/10.1099/mgen.0.000878

[2]

Lam, M.M.C., Wick, R.R., Judd, L.M., Holt, K.E., Wyres, K.L., 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

[3]

Van Der Graaf-van Bloois, L., Chen, H., Wagenaar, J.A., Zomer, 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

[4]

Wick, R.R., Heinz, E., Holt, K.E., Wyres, K.L., 2018. Kaptive Web: 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

[5]

Wyres, K.L., Cahill, S.M., Holt, K.E., Hall, R.M., Kenyon, J.J., 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

[6]

Wyres, K.L., Wick, R.R., Gorrie, C., Jenney, A., Follador, R., 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