Genetic characteristics of clinical carbapenem-resistant Klebsiella pneumoniae: epidemic ST11 KPC-2-producing strains and non-negligible NDM-5-producing strains with diverse STs

Abstract

Abstract Klebsiella pneumoniae is among the most important Gram-negative pathogens that can cause serious nosocomial infections. The emergence and prevalence of hypervirulent carbapenem-resistant K. pneumoniae (Hv-CRKP) pose a significant challenge to public health. In this study, we characterized thirty carbapenem-resistant K. pneumoniae (CRKP) strains from a tertiary care hospital in Sichuan province, China, by whole-genome sequencing and genome analysis. These strains were all highly resistant to carbapenem but remained susceptible to tigecycline. Of the 30 tested CRKP strains, 23 were positive for bla KPC−2 and seven for bla NDM−5. These bla KPC−2-positive strains all belonged to ST11, while bla NDM−5-positive strains belonged to five distinct STs. Phylogenetic analysis revealed a predominant intra-hospital transmission of ST11-KL64 in KPC-2-producing CRKP, and that both clonal and horizontal transmission of bla NDM−5 have occurred among NDM-5-producing CRKP strains in this hospital. Hypervirulence genes were commonly detected in the CRKP. The prevalent pLVKP-like plasmid and ICEKp seem to have contributed largely to the transmission of virulence genes in them. bla NDM−5 was located on highly similar IncX3 plasmids in the collected strains, and its truncated vision was highlighted. bla KPC−2 was primarily carried by IncFII/IncR plasmids in our collection. At least two IncFII/IncR plasmid subtypes were identified, exhibiting high similarity to many previously reported bla KPC−2-bearing plasmids from different parts of China. The findings provide an expanded knowledge of the genetic characteristics of CRKP, the transmission pattern of carbapenem-resistance genes, and also the convergence of Hv-CRKP.

Keywords

• CRKP
• bla KPC−2
• bla NDM−5
• Hypervirulence
• IncFII/IncR plasmid