Microbial Characteristics and Genomic Analysis of an ST11 Carbapenem-Resistant Klebsiella pneumoniae Strain Carrying bla(KPC−2) Conjugative Drug-Resistant Plasmid

BACKGROUND: The sequence type 11 (ST11) carbapenem-resistant Klebsiella pneumoniae (CRKP) carrying bla(KPC−2) has been widespread all over the world, and it has been reported frequently in China. The bla(KPC−2) located on the mobile genetic element brings tremendous pressure to control the spread and outbreak of resistant bacteria. Whole-genome sequencing (WGS) technology can comprehensively and in-depth display the molecular characteristics of drug-resistant bacteria, providing a basis for evaluating the genetic diversity within the CRKP genome. METHODS: The ST11 CRKP in this study was collected in the intensive care unit of a major teaching hospital. PCR and Sanger sequencing confirmed the existence of bla(KPC−2). The AST-GN card and the microbroth dilution test were used for antimicrobial susceptibility testing. The transferability of plasmid was verified by a conjugation test. The whole genome is sequenced using the Illumina HiSeq short-read and Oxford Nanopore long-read sequencing technology. RESULTS: The studied strain was named CRKP63, which is a multi-drug resistance bacteria, which carries bla(KPC−2) and bla(SHV−182). Its genome consists of a circular chromosome of 5,374,207 bp and an IncFII plasmid named pKPC-063001 of 359,625 bp. In the drug-resistant plasmid pKPC-063001, the key carbapenem resistance gene bla(KPC−2) was located in the genetic context with insertion sequence ISKpn27 upstream and ISKpn6 downstream and bracketed by IS26. The three copies of the IS26–ISKpn27–bla(KPC−2)–ISKpn6–IS26 unit were present in tandem. bla(KPC−2) can be transferred horizontally between other species by conjugation, the complete type IV secretion system (T4SS) structure helps to improve the adaptability of bacteria to the external environment, strengthen the existence of drug-resistant bacteria, and accelerate the spread of drug resistance. CONCLUSION: High-throughput sequencing has discovered the different surrounding environments of bla(KPC−2), which provides a new idea for further revealing the transmission and inheritance of bla(KPC−2) at the molecular level. In order to control the further spread and prevalence of drug-resistant bacteria, we should pay close attention to the changes in the genetic environment of bla(KPC−2) and further study the transcription and expression of T4SS.