Genomic architecture of fourth-generation cephalosporin-resistant Klebsiella pneumoniae Species Complex (KpSC) from patients and their hospital environment in Uganda
Loading...
Date
2026-06-01
Journal Title
Journal ISSN
Volume Title
Publisher
Springer Nature
Abstract
The emergence of fourth-generation cephalosporin-resistant (4GCR) K. pneumoniae species complex (KpSC) is a human health concern due to limited therapeutic options and association of the bacteria with severe morbidity and mortality. This study investigated the genomic characteristics of 4GCR K. pneumoniae species complex strains from patients and their hospital environment in Uganda. Twenty-seven isolates were obtained from two tertiary healthcare hospitals in Uganda. Whole genomic sequence (WGS) analysis revealed dominance of phylogroup Kp1 (70.4%). Isolates were highly diverse genetically, representing 15 clonal groups and 10 different serotypes, with isolates of CG17 (6/27) and serotype O5 (25%) as the most common. Core genome SNP-based phylogenetic comparison placed Ugandan strains together with strains from African lineages; however, with a few strains clustering with global references. Most strains carried multiple resistance genes, particularly CTX-M-15 (24/27) and aminoglycoside-modifying enzymes. A search for virulence factors revealed that most isolates carried few virulence genes, particularly those associated with hypervirulence. A yersiniabactin loci was detected in a subset of Kp1 isolates. Ten plasmid replicons and multiple insertion sequences were detected that may mediate resistance dissemination. These findings provide evidence of 4GCR KpSC in clinical settings and patient environments in Uganda. This underscores the need for ongoing genomic surveillance and antimicrobial stewardship to enable early detection of resistant strains and prevent localized clusters from escalating into widespread outbreaks in hospitals across the country.
Description
This study advances SDG 3 (Good Health and Well-being), Target 3.d, by improving detection, monitoring, and control of antimicrobial-resistant pathogens. It also supports SDG 9 (Industry, Innovation and Infrastructure), Target 9.5, through applying whole-genome sequencing to promote health research and innovation. Furthermore, the study contributes to SDG 17 (Partnerships for the Goals), Target 17.6, by fostering scientific collaboration and facilitating technology transfer for genomic surveillance. The research aligns with Uganda’s National Development Plan IV (NDP IV), especially the Human Capital Development Programme, which emphasizes disease prevention, improved healthcare, and health security. It also supports the Science, Technology and Innovation Programme, which encourages research-driven solutions to national challenges. By investigating fourth-generation cephalosporin-resistant Klebsiella pneumoniae in Ugandan hospitals, this work generates evidence to inform antimicrobial stewardship, infection prevention and control, and genomic surveillance. The findings support policy development to enhance patient safety, strengthen healthcare systems, and improve Uganda’s preparedness for antimicrobial resistance.
Keywords
Antimicrobial-resistant, Carbapenem-resistant, Enterobacteriaceae, Antimicrobial surveillance
Citation
Byarugaba, D. K., Wokorach, G., Hounmanou, Y. M., Wanyana, A., Alafi, S., Wabwire-Mangen, F., ... & Olsen, J. E. (2026). Genomic architecture of fourth-generation cephalosporin-resistant Klebsiella pneumoniae Species Complex (KpSC) from patients and their hospital environment in Uganda. BMC microbiology.