Genomic and phenotypic characterization of ST2012 clinical Klebsiella quasipneumoniae subsp. similipneumoniae harboring bla NDM−1 in China

Abstract Background Klebsiella pneumoniae has emerged as a significant pathogen that causes community and hospital infections due to its high resistance rate and transmissibility. Klebsiella pneumoniae complex is classified into three phylogroups: Klebsiella pneumoniae (KpI), Klebsiella quasipneumoniae (KpII), and Klebsiella variicola (KpIII) in classical taxonomy, but KpII and KpIII are infrequently isolated clinically. Although pathogenic KpII has been reported worldwide, the understanding of this pathogen remains limited. Methods Whole-genome sequencing (WGS) of K. quasipneumoniae subsp. similipneumoniae ACESH00366hy was performed. Plasmid characterization was demonstrated using S1-PFGE, Southern blotting, and conjugation assays. Antimicrobial susceptibility testing was performed and interpreted according to CLSI, EUCAST, and FDA standards. The virulence of the strain was assessed using the Galleria mellonella infection assay, serum-killing assay, and biofilm formation assay. A phylogenetic tree was constructed to explore its biological evolution. Results The K. quasipneumoniae subsp. similipneumoniae isolate ACESH00366hy, belonging to ST2012 and KL139, contains several resistance genes including bla NDM−1, bla SHV−12, bla OKP−B−2, and oqxAB, as well as various virulence genes including iroE, iutA, mrkABCDFHIJ, entABCDEFS, and fepABCDG. The bla NDM−1 and bla SHV−12 genes were present on the 53,624 bp IncX3 plasmid. Virulence assays showed that the virulence of ACESH00366hy was greater than that of the low-toxicity strain ATCC 700,603. Phylogenetic analysis demonstrated the emergence of ST2012 KpII-B in Asia and revealed the spread of K. quasipneumoniae subsp. similipneumoniae in humans, animals, and the environment. Conclusion This study highlights the emergence of clinical ST2012 KpII strains harbouring bla NDM−1 via the IncX3 plasmid in China. We evaluated its resistance and virulence characteristics and performed phylogenetic analysis, thereby enhancing our understanding of its resistance and pathogenicity and contributing to the clinical surveillance of K. quasipneumoniae.