Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana

Comprehensive data on the genomic epidemiology of hospital-associated Klebsiella pneumoniae in Ghana is scarce. This study sequenced 103 clinical K. pneumoniae isolates from five tertiary hospitals in Southern Ghana, predominantly from paediatric patients under five years (67/103, 65%), with the majority collected from urine (32/103, 31%) and blood (25/103, 24%) cultures. We employed Pathogenwatch for genotyping via Kaptive (K/O antigens) and Kleborate (antimicrobial resistance and hypervirulence) and determined clonal relationships using core-genome multilocus sequence typing (cgMLST). Among the 44 distinct sequence types (STs) detected, ST133 was the most common, comprising 23% of isolates (n=23/103). We discovered 27 different capsular (K) locus antigens and seven lipopolysaccharide (O) types; KL116 (28/103, 27%) and O1 (66/103, 64%) were the most prevalent. Single-linkage clustering highlighted the global spread of multidrug-resistant clones such as ST15, ST307, ST17, ST11, ST101, and ST48, with minimal allele differences (1-5) from publicly available genomes worldwide. Conversely, several isolates (n=17) constituted novel clonal groups and lacked close relatives among publicly available genomes, displaying unique genetic diversity within our study population. A significant proportion of isolates (88/103, 85%) carried resistance genes for three or more antibiotic classes, with the blaCTXM-15 gene present in 78% (n=80/103). Carbapenem resistance, predominantly due to blaOXA-181 and blaNDM-1 genes, was found in 10% (n=10/103) of the isolates. Yersiniabactin was the predominant acquired virulence trait, identified in 70% (n=72/103) of the isolates. Our findings reveal a complex genomic landscape of K. pneumoniae in Southern Ghana, underscoring the critical need for ongoing genomic surveillance to manage the substantial burden of antimicrobial resistance.