Genomic a Nalysis and Molecular Characteristics in Carbapenem R Esistant Klebsiella Pneumoniae Strains

Abstract

Background Klebislla 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. Methods Whole-genome sequencing of one strain was performed using the Illumina Hiseq and PacBio RS systems. Genomic information was comprehensively analyzed by various bioinformatics approaches. Molecular typing was based on multi locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) analysis. Antimicrobial susceptibility testing, drug resistance and virulence genes were determined. Results K. pneumoniae KPX comprised one circular chromosome and four circular plasmids. This strain harbors a variety of antimicrobial resistance and virulence determinants. The closest relative of K. pneumoniae KPX was another ST11 clinical isolate recovered Sichuan. Fifty isolates were phenotypically confirmed extended-spectrum beta-lactamases ESBLs producers. MLST analysis revealed 97% sequence type 11. Fifty Carbapenem Resistant isolates mainly belong to three clones according to the PFGE DNA patterns. PFGE patterns has more variety than ST profiles. 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%), iucABCD(10%), and rmpA2 (100%) genes were presented in multiple drug resistant strains. Conclusion The dataset presented in this study provided the genomic and epidemiological analysis of Carbapenem Resistant K. pneumoniae in hospital settings. Antimicrobial-resistance profiles suggested the presence of significant selective antibiotic pressure. Appropriate surveillance is essential to development of effective control strategies in the prevention of nosocomial infection.