Extensively Drug-Resistant ST16 Klebsiella pneumoniae Co-Harboring bla KPC-2, bla OXA-181, and Chromosomal bla NDM-4: Genomic Features and Therapeutic Challenges.

PURPOSE: Carbapenem-resistant Klebsiella pneumoniae (CRKP) represents a major global public health threat due to its high-level antimicrobial resistance and limited therapeutic options. The emergence of CRKP isolates co-harboring multiple carbapenemase genes further complicates clinical management and infection control. This study aimed to characterize the antimicrobial resistance phenotype, complete genomic features, and carbapenemase gene environments of an extensively drug-resistant ST16 CRKP bloodstream isolate co-harboring class A, B, and D carbapenemases.

METHODS

A CRKP isolate, designated KPY1, was recovered from the bloodstream of an intensive care unit patient. Antimicrobial susceptibility testing was performed to determine the resistance phenotype. Whole-genome sequencing was conducted using a hybrid Illumina-Nanopore approach. Genome assembly, antimicrobial resistance gene detection, plasmid replicon typing, comparative plasmid analysis, and genetic environment analysis of carbapenemase genes were performed using established bioinformatic tools.

RESULTS

KPY1 belonged to sequence type 16 and exhibited an extensively drug-resistant phenotype, including resistance to carbapenems, β-lactam/β-lactamase inhibitor combinations, ceftazidime-avibactam, and colistin. Genomic analysis revealed the coexistence of three carbapenemase genes: bla KPC-2, bla NDM-4, and bla OXA-181. Notably, bla NDM-4 was located on the chromosome and flanked by two IS26 elements, suggesting a possible IS26-associated rearrangement event. In contrast, bla KPC-2 was located on an IncFII(K) plasmid within a Tn3-family transposon structure, whereas bla OXA-181 was carried by a conserved ColKP3-IncX3 plasmid backbone.

CONCLUSION

This study describes a rare and clinically challenging ST16 CRKP bloodstream isolate co-harboring class A, B, and D carbapenemases. The chromosomal integration of bla NDM-4 may contribute to stable maintenance of carbapenem resistance, while the coexistence of multiple carbapenemase determinants highlights the value of complete genome sequencing for resolving complex resistance configurations and supporting surveillance of high-risk CRKP lineages.