Klebsiella pneumonia in Sudan: Multidrug Resistance, Polyclonal Dissemination, and Virulence
Einas A Osman1, Maho Yokoyama2, Hisham N Altayb3
1Bioscience Research Institute, Ibn Sina University, Khartoum 11111, Sudan.
Abstract:
The emergence and global expansion of hyper-virulent and multidrug resistant (MDR) Klebsiella pneumoniae is an increasing healthcare threat worldwide. The epidemiology of MDR K. pneumoniae is under-characterized in many parts of the world, particularly Africa. In this study, K. pneumoniae isolates from hospitals in Khartoum, Sudan, have been whole-genome sequenced to investigate their molecular epidemiology, virulence, and resistome profiles. Eighty-six K. pneumoniae were recovered from patients in five hospitals in Khartoum between 2016 and 2020. Antimicrobial susceptibility was performed by disk-diffusion and broth microdilution. All isolates underwent whole genome sequencing using Illumina MiSeq; cgMLST was determined using Ridom SeqSphere+, and 7-loci MLST virulence genes and resistomes were identified. MDR was observed at 80%, with 35 isolates (41%) confirmed carbapenem-resistant. Thirty-seven sequence types were identified, and 14 transmission clusters (TC). Five of these TCs involved more than one hospital. Ybt9 was the most common virulence gene detected, in addition to some isolates harbouring iuc and rmp1. There is a diverse population of K. pneumoniae in Khartoum hospitals, harbouring multiple resistance genes, including genes coding for ESBLs, carbapenemases, and aminoglycoside-modifying enzymes, across multiple ST's. The majority of isolates were singletons and transmissions were rare.
Insights
Multidrug-resistant Klebsiella pneumoniae strains are a global threat. This study reveals a diverse population of these bacteria in Khartoum hospitals, Sudan, with high rates of antimicrobial resistance and rare transmissions.
Area of Science:
- Microbiology
- Genomics
- Epidemiology
Background:
- Hyper-virulent and multidrug-resistant (MDR) Klebsiella pneumoniae poses a significant global healthcare challenge.
- The epidemiology of MDR K. pneumoniae remains under-characterized in many regions, particularly in Africa.
Purpose of the Study:
- To investigate the molecular epidemiology, virulence, and resistome profiles of K. pneumoniae isolates from hospitals in Khartoum, Sudan.
- To characterize the genetic diversity and antimicrobial resistance patterns of K. pneumoniae in this understudied region.
Main Methods:
- Whole-genome sequencing of 86 K. pneumoniae isolates recovered from five hospitals in Khartoum (2016-2020).
- Antimicrobial susceptibility testing (disk-diffusion and broth microdilution).
- Analysis of sequence types (STs), transmission clusters (TCs), virulence genes, and resistomes using cgMLST and 7-loci MLST.
Main Results:
- 80% of isolates were MDR, with 41% confirmed carbapenem-resistant.
- Thirty-seven distinct sequence types were identified, forming 14 transmission clusters, with five TCs spanning multiple hospitals.
- The most common virulence gene was Ybt9; isolates also harbored iuc and rmp1. A diverse array of resistance genes, including those for ESBLs, carbapenemases, and aminoglycoside-modifying enzymes, were detected across multiple STs.
- The majority of isolates were singletons, indicating rare transmission events.
Conclusions:
- Khartoum hospitals harbor a genetically diverse population of K. pneumoniae.
- These isolates possess a wide range of antimicrobial resistance genes, contributing to the growing threat of MDR pathogens.
- While transmissions appear rare, the presence of diverse and resistant strains highlights the need for enhanced surveillance and control measures.
