Deciphering the Epidemiological Characteristics and Molecular Features of bla(KPC–2)- or bla(NDM–1)-Positive Klebsiella pneumoniae Isolates in a Newly Established Hospital

The emergence of hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) was regarded as an emerging threat in clinical settings. Here, we investigated the prevalence of CRKP strains among inpatients in a new hospital over 1 year since its inception with various techniques, and carried out a WGS-based phylogenetic study to dissect the genomic background of these isolates. The genomes of three representative bla(NDM–1)-positive strains and the plasmids of four bla(KPC–2)-positive strains were selected for Nanopore long-read sequencing to resolve the complicated MDR structures. Thirty-five CRKP strains were identified from 193 K. pneumoniae isolates, among which 30 strains (85.7%) harbored bla(KPC–2), whereas the remaining five strains (14.3%) were positive for bla(NDM–1). The antimicrobial resistance profiles of bla(NDM–1)-positive isolates were narrower than that of bla(KPC–2)-positive isolates. Five isolates including two bla(NDM–1)-positive isolates and three bla(KPC–2)-positive strains could successfully transfer the carbapenem resistance phenotype by conjugation. All CRKP strains were categorized into six known multilocus sequence types, with ST11 being the most prevalent type. Phylogenetic analysis demonstrated that the clonal spread of ST11 bla(KPC–2)-positive isolates and local polyclonal spread of bla(NDM–1)-positive isolates have existed in the hospital. The bla(NDM–1) gene was located on IncX3, IncFIB/IncHI1B, and IncHI5-like plasmids, of which IncFIB/IncHI1B plasmid has a novel structure. By contrast, all ST11 isolates shared the similar bla(KPC–2)-bearing plasmid backbone, and 11 of them possessed pLVPK-like plasmids. In addition, in silico virulome analysis, Galleria mellonella larvae infection assay, and siderophore secretion revealed the hypervirulence potential of most bla(KPC–2)-positive strains. Given that these isolates also had remarkable environmental adaptability, targeted measures should be implemented to prevent the grave consequences caused by hv-CRKP strains in nosocomial settings.