Genomic Analysis and Molecular Characteristics in Carbapenem-Resistant Klebsiella pneumoniae Strains

Klebsiella pneumoniae is an important bacterium and responsible for both infections acquired in hospital and community because of its multidrug resistance and the virulence. The aim of this research was to investigate clonal lineages, antibiotic resistance profiles, and virulence factors of the hospital isolated carbapenem-resistant strains. Fifty carbapenem-resistant isolates were phenotypically confirmed extended-spectrum beta-lactamases ESBLs producers. MLST analysis revealed 94% sequence type 11. These isolates mainly belonged to three clones according to the PFGE DNA patterns. PFGE patterns have good discrimination than ST profiles. One isolate, K. pneumoniae KPX, undergoing whole-genome sequencing comprised one circular chromosome and four circular plasmids. This isolate harbored a variety of antimicrobial resistance and virulence determinants. The closest relative of K. pneumoniae KPX was another ST11 clinical isolate recovered Sichuan. In addition, KPC-2 (98.0%), SHV-11 (98.0%), TEM-1 (76.0%), CTX-M (76.0%), oqxB1(66%), qnrS (70%), Int1 (42.0%), sul1 (82.0%), sul2 (96.0%), iutA (88%), iucC(10%), and rmpA2 (100%) genes were presented in multiple drug-resistant isolates. The dataset presented in this study provided the genomic and epidemiological analysis of carbapenem-resistant K. pneumoniae in hospital settings. Antimicrobial-resistant profiles suggested the presence of significant selective antibiotic pressure. Appropriate surveillance is essential to the development of effective control strategies in the prevention of nosocomial infection.