First identification of an ST11-KL64 hypervirulent Klebsiella pneumoniae strain coproducing KPC-2 and NDM-1 with an OmpK36 GD mutation

Introduction The convergence of hypervirulence and carbapenem resistance in Klebsiella pneumoniae represents a critical clinical threat. Methods We characterized 27 NDM-producing K. pneumoniae isolates collected from a tertiary hospital in Lishui, China, between 2017 and 2023. Among the isolates, we selected an ST11 strain, CRKP26, carrying bla KPC-2 and bla NDM-1 , for further investigation using whole-genome sequencing (WGS) and phenotypic assays. Results The surveillance detected high clonal diversity across 19 sequence types among the isolates. CRKP26 exhibited extensive drug resistance, with resistance to ceftazidime, cefepime, aztreonam, piperacillin-tazobactam, and amikacin and high-level carbapenem resistance, with MICs of 64 μg/mL for imipenem and 256 μg/mL for meropenem. This strain was susceptible only to polymyxin B and tigecycline. Whole-genome sequencing (WGS) of CRKP26 revealed that bla KPC-2 and bla NDM-1 were located on separate plasmids and that insertion of glycine–aspartate (GD) at positions 137–138 was identified in the ompK36 gene. WGS further identified CRKP26 as capsular serotype KL64 and confirmed the presence of core virulence determinants, including the aerobactin operon ( iucABCD - iutA ), on an IncFIB virulence plasmid. Strain CRKP26 was defined as hypervirulent (LD 50 ≤ 1 × 10 6 CFU), despite showing slightly attenuated lethality compared to the classic hypervirulent strain NTUH-K2044. Furthermore, the survival rate of CRKP26 was 93.2% in serum killing assays and 90.7% in neutrophil killing assays, comparable to that of the hypervirulent control NTUH-K2044. Conclusion To our knowledge, this is the first report of a hypervirulent ST11-KL64 K. pneumoniae strain carrying both bla KPC-2 and bla NDM-1 with an OmpK36 GD mutation. This convergence of plasmid-mediated resistance, chromosomal mutation, and hypervirulence in a high-risk clone highlights an urgent threat requiring increased genomic surveillance.