Genomic Characteristics of Klebsiella pneumoniae Isolates in Kenya: Serotypes, Sequence Types, Antimicrobial Resistance, Virulence, and Phylogeny

Abstract

Klebsiella pneumoniae is a globally important opportunistic pathogen associated with both healthcare-associated and community-acquired infections. In Kenya, limited knowledge of its genomic characteristics hinders efforts to detect, treat, and control multidrug-resistant strains. This study analyzed 89 K. pneumoniae isolates collected over six years from eight hospitals in five counties (Kisumu, Kericho, Kilifi, Kisii, and Nairobi) to characterize their phenotypic antimicrobial susceptibility, multidrug resistance, geographic distribution, and genomic features, including serotypes, sequence types, antimicrobial resistance and virulence genes, and phylogenetic relationships. Isolates were obtained from community-acquired infections (62/89) – infections occurring within 48 hours of patient admission, healthcare-associated infections (21/89) – infections occurring after 48 hours of patient admission or among healthcare workers, and the hospital environment (6/89) – isolates obtained from hospital high touch surfaces and analyzed using Illumina and Nanopore whole-genome sequencing. The genomes were screen for several gene features: antimicrobial resistance genes (CARD), virulence genes (Kaptive), multilocus sequence types (mlst) K-locus and O-antigen serotypes (Kaptive) analyzed, plasmid replicons (Plasmidfinder) and plasmid classification (Plascard). The phylogenetic tree of the 89 study isolates alone (parsnp) and when combined with 6286 global isolate representatives from the BV-BRC database (Mash) was generated and the trees were edited using iToL. A total of 38 sequence types were identified, including globally disseminated high-risk clones (ST14, ST15, ST147, and ST307) and the regionally important ST17. The community-acquired infection isolates have a higher antibiotic burden than the healthcare-associated infection isolates (p= < 0.05) while the healthcare-associated infection isolates have a slightly higher virulence burden than the healthcare-associated isolates (p = > 0.05). Phylogenetic analysis showed that Kenyan isolates were interspersed with global strains, suggesting either long-term global circulation or recent introduction from external sources. Genomic analysis revealed the presence of carbapenemase genes (blaNDM-1 and blaOXA-181), pan-aminoglycoside resistance genes (armA and rmtF), and extended-spectrum beta-lactamase genes, predominantly blaCTX-M-15 (36/89), blaTEM (35/89), and blaOXA (18/89). A mobile colistin resistance gene (mcr-8) was identified in one isolate, and fluoroquinolone resistance-associated mutations in gyrA and parC were detected. Key virulence factors included regulators of hypervirulence (rmpA/A2 and magA) and siderophores such as yersiniabactin, salmochelin, and aerobactin. Notably, two potential hypervirulent isolates and two community-acquired ST147 high-risk clones carried both carbapenemase genes and virulence determinants. Plasmids played a central role in the dissemination of antimicrobial resistance and virulence genes through conjugation. Overall, these findings demonstrate that Kenyan K. pneumoniae isolates harbor diverse resistance and virulence profiles, including high-risk clones with the potential for rapid spread. This underscores the need for expanded national surveillance integrating genomic and phenotypic data across clinical and environmental settings to better monitor and control emerging threats.