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Genomic Characterization of Klebsiella pneumoniae Causing Invasive Disease in South African Infants: Observational

Courtney P Olwagen1, Alane Izu1, Shama Khan1

  • 1South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa.

Open Forum Infectious Diseases
|January 26, 2026
PubMed

Insights

Genomic sequencing of invasive Klebsiella pneumoniae in African infants revealed dominant strains and high multidrug resistance, including carbapenem resistance. Findings highlight key targets for potential vaccine development against this critical pathogen.

Area of Science:

  • Microbiology
  • Genomics
  • Epidemiology

Background:

  • Klebsiella pneumoniae (KPn) is a major cause of invasive bacterial disease in African children.
  • There is limited genotypic characterization of KPn strains causing invasive disease in this population.

Purpose of the Study:

  • To perform genotypic characterization of invasive Klebsiella pneumoniae isolates from infants in Africa.
  • To identify dominant strains, antimicrobial resistance patterns, and potential vaccine targets.

Main Methods:

  • Whole-genome sequencing of 337 invasive KPn isolates from infants (≤90 days) collected via hospital surveillance and postmortem sampling.
  • Genomic analysis to determine clonotypes, sequence types (STs), K-loci (KLs), and O-antigens.
  • Detection of antimicrobial resistance genes, including those conferring carbapenem resistance.

Main Results:

  • Sequence type 17 (22.0%) and ST39 (12.7%) were the predominant clonotypes.
  • Dominant K-loci included KL25 (24.0%), KL2 (14.5%), and KL149 (13.4%), with O1αβ,2α and O5 as major O-antigens.
  • Eighty-five percent of isolates harbored multidrug resistance genes; 32.9% showed carbapenem resistance, with blaOXA-181 being the most common carbapenemase gene.

Conclusions:

  • Invasive KPn disease in African infants is associated with diverse strains, but over 80% are linked to 11 K-loci.
  • These findings offer crucial insights into KPn epidemiology in African children.
  • The identified K-loci represent potential targets for vaccine development to combat invasive KPn infections.
Abstract

Keywords:
Klebsiella pneumoniae-associated deathsmultidrug resistanceneonatal sepsisserious bacterial infectionvaccine

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