Published June 25, 2025 | Version v1
Technical note Open

Technical Report: Accuracy of Klebsiella pneumoniae capsule serotype predictions from whole genome sequences

Authors/Creators

  • 1. EDMO icon Monash University
  • 2. ROR icon Statens Serum Institut
  • 3. ICMR-National Institute for Research in Bacterial Infections
  • 4. ROR icon Children's Hospital of Philadelphia
  • 5. University of the Witwatersrand Johannesburg
  • 6. ROR icon University of St Andrews
  • 7. ROR icon University of Strathclyde
  • 8. University of Abuja College of Health Sciences
  • 9. ROR icon National Hospital Abuja
  • 10. ROR icon University of the Witwatersrand
  • 11. University of the Witwatersrand Johannesburg Faculty of Science
  • 12. University of Witwatersrand / South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit
  • 13. ROR icon Child Health Research Foundation
  • 14. ROR icon University of Oxford
  • 15. ROR icon Quaid-i-Azam University
  • 16. London School of Hygiene and Tropical Medicine Faculty of Infectious and Tropical Diseases

Abstract

Klebsiella pneumoniae is a priority pathogen for the development of novel therapeutic and prophylactic measures such as vaccines and monoclonal antibody therapies. Key molecular targets include the polysaccharide capsule, which protects K. pneumoniae from phagocytosis and serum bactericidal activity, and is highly immunogenic. A total of 77 distinct serological phenotypes have been defined but more than 160 different capsule polysaccharides are predicted based on analysis of the corresponding capsule (K) biosynthesis loci from whole genome sequences (WGS). These loci form the basis for WGS-based capsule typing with the computational tool, Kaptive, enabling capsule epidemiology investigations at scale to inform vaccine design. However, to-date limited data has been available with which to assess the accuracy of Kaptive for phenotype inference. 

Here we present a preliminary analysis of 731 matched serological and genomic K-type calls, and show that 84.5% of the serotypes are concordant with genomic predictions, supporting use of Kaptive for seroepidemiology analyses. Ongoing work will expand the dataset, investigate genotype-phenotype discrepancies and update Kaptive to further improve its accuracy.

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Stanton_2025_Technical_Report_Accuracy_of_Klebsiella_pneumoniae_capsule_serotype_predictions_from_whole_genome_sequences.pdf

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Additional details

Funding

Bill & Melinda Gates Foundation
INV049641
Bill & Melinda Gates Foundation
INV025304
Bill & Melinda Gates Foundation
INV005180
Bill & Melinda Gates Foundation
INV005773
Wellcome Sanger Institute
206454
Wellcome Trust
217303/Z/19/Z
National Health and Medical Research Council
APP1176192