Pathogens (Nov 2023)

Genome Analysis of <i>Klebsiella pneumoniae</i> Reveals International High-Risk Pandemic MDR Clones Emerging in Tertiary Healthcare Settings in Uganda

  • Denis K. Byarugaba,
  • Bernard Erima,
  • Godfrey Wokorach,
  • Stephen Alafi,
  • Hannah Kibuuka,
  • Edison Mworozi,
  • Florence Najjuka,
  • James Kiyengo,
  • Ambrose K. Musinguzi,
  • Fred Wabwire-Mangen

DOI
https://doi.org/10.3390/pathogens12111334
Journal volume & issue
Vol. 12, no. 11
p. 1334

Abstract

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Klebsiella pneumoniae is a threat to public health due to its continued evolution. In this study, we investigated the evolution, convergence, and transmission of hypervirulent and multi-drug resistant (MDR) clones of K. pneumoniae within healthcare facilities in Uganda. There was high resistance to piperacillin (90.91%), cefuroxime (86.96%), ceftazidime (84.62%), cefotaxime (84.00%), amoxicillin/clavulanate (75%), nalidixic acid (73.68%), and nitrofurantoin (71.43%) antibiotics among K. pneumoniae isolates. The isolates were genetically diverse, consisting of 20 different sequence types (STs) and 34 K-serotype groups. Chromosomal fosA (for fosfomycin) and oqxAB efflux pump genes were detected in all isolates. Two carbapenem resistance genes, blaNDM-5 and blaOXA-181 plus extended-spectrum beta-lactamase (blaCTX-M-15) gene (68.12%), quinolone-resistant genes qnrS1 (28.99%), qnrB1 (13.04%), and qnrB6 (13.04%) and others were found. All, except three of the isolates, harbored plasmids. While the isolates carried a repertoire of virulence genes, only two isolates carried hypervirulent genes demonstrating a low prevalence (2.90%) of hypervirulent strains. Our study demonstrated genetically diverse populations of K. pneumoniae, low levels of carbapenem resistance among the isolates, and no convergence of MDR and hypervirulence. Emerging high-risk international pandemic clones (ST11, ST14, ST147, ST 86 and ST307) were detected in these healthcare settings which are difficult to treat.

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