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Volume 8, Issue 3

Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the species complex Open Access

Abstract

The outer polysaccharide capsule and lipopolysaccharide (LPS) antigens are key targets for novel control strategies targeting and related taxa from the species complex (KpSC), including vaccines, phage and monoclonal antibody therapies. Given the importance and growing interest in these highly diverse surface antigens, we had previously developed Kaptive, a tool for rapidly identifying and typing capsule (K) and outer LPS (O) loci from whole genome sequence data. Here, we report two significant updates, now freely available in Kaptive 2.0 (https://github.com/katholt/kaptive): (i) the addition of 16 novel K locus sequences to the K locus reference database following an extensive search of >17 000 KpSC genomes; and (ii) enhanced O locus typing to enable prediction of the clinically relevant O2 antigen (sub)types, for which the genetic determinants have been recently described. We applied Kaptive 2.0 to a curated dataset of >12 000 public KpSC genomes to explore for the first time, to the best of our knowledge, the distribution of predicted O (sub)types across species, sampling niches and clones, which highlighted key differences in the distributions that warrant further investigation. As the uptake of genomic surveillance approaches continues to expand globally, the application of Kaptive 2.0 will generate novel insights essential for the design of effective KpSC control strategies.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): K locus , Klebsiella capsule K-locus genomic surveillance , Klebsiella pneumoniae and O locus
Funding
This study was supported by the:
  • National Health and Medical Research Council (Award APP1176192)
    • Principle Award Recipient: KellyL. Wyres
  • Bill and Melinda Gates Foundation (Award INV023041)
    • Principle Award Recipient: KathrynE. Holt
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2022-03-21
2024-04-27
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Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex
M Gen 8, 000800 (2022); https://doi.org/10.1099/mgen.0.000800
/content/journal/mgen/10.1099/mgen.0.000800
/content/journal/mgen/10.1099/mgen.0.000800
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