PCR-based ORF typing of Klebsiella pneumoniae for rapid identification of global clones and transmission events

Aims Klebsiella pneumoniae is a major cause of healthcare-associated infections. In this study, we aimed to develop a rapid and simple genotyping method that can characterize strains causing nosocomial infections. Methods and results The PCR-based open reading frame (ORF) typing (POT) method consists of two multiplex PCR reactions that were designed to detect 25 ORFs specific to bacterial genetic lineages, species, antimicrobial-resistant genes (bla(CTX-M group-1), bla(CTX-M group-9), bla(IMP) and bla(KPC)), a capsular K1-specific gene and a virulence factor gene (rmpA/A2). The electrophoresis results are then digitized. A total of 192 strains (136 clinical and 8 reference strains of K. pneumoniae, 33 clinical and 1 reference strains of K. variicola and 14 clinical strains of K. quasipneumoniae) were classified into 95, 26 and 11 POT values, respectively. The distribution patterns of ORFs among K. pneumoniae correlated well with multilocus sequence typing (MLST). Furthermore, closely related species could be distinguished and key antimicrobial resistance and hypervirulence genes were identified as part of POT. Conclusions The POT method was developed and validated for K. pneumoniae. In comparison to MLST, the POT method is a rapid and easy genotyping method for monitoring transmission events by K. pneumoniae in clinical microbiology laboratories. Significance and Impact of the Study The POT method supplies clear and informative molecular typing results for K. pneumoniae. The method would facilitate molecular epidemiological analysis in infection control and hospital epidemiology investigations.

Automated summary

The study developed a rapid and simple genotyping method for Klebsiella pneumoniae, called PCR-based open reading frame typing (POT), which was validated for 192 strains in clinical settings. The distribution patterns of ORFs among K. pneumoniae correlated well with multilocus sequence typing (MLST), enabling the identification of closely related species and key antimicrobial resistance and hypervirulence genes as part of POT. The POT method is a valuable tool for monitoring transmission events and facilitating molecular epidemiological analysis in infection control and hospital epidemiology investigations.