Genomic architecture of fourth-generation cephalosporin-resistant Klebsiella pneumoniae Species Complex (KpSC) from patients and their hospital environment in Uganda.

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.