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

• Published in: Journal of applied microbiology 2022-09, Vol.133 (3), p.2050-2062
• Main Authors: Nonogaki, Rina, Iijima, Anna, Kawamura, Kumiko, Kayama, Shizuo, Sugai, Motoyuki, Yagi, Tetsuya, Arakawa, Yoshichika, Doi, Yohei, Suzuki, Masahiro
• Format: Article
• Language: English
• Subjects: Antimicrobial agents; Antimicrobial resistance; Clinical microbiology; Distribution patterns; Electrophoresis; Epidemiology; Genes; Genotyping; infection control; Klebsiella; Klebsiella pneumoniae; Microbiology; MLST; Multilocus sequence typing; multiplex PCR; Nosocomial infection; Nosocomial infections; Open reading frames; Strains (organisms); Virulence factors
• ISSN: 1364-5072; 1365-2672
• DOI: 10.1111/jam.15701

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 (blaCTX‐M group‐1, blaCTX‐M group‐9, blaIMP and blaKPC), 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.