Unravelling the genome sequence of NDM-1- and KPC-2-co-producing Klebsiella pneumoniae ST11 isolated from a bloodstream infection

Abstract Objectives The resistance rate of Klebsiella pneumoniae to commonly used antibiotics has been increasing rapidly and has caused serious concern among clinicians and microbiologists. Resistance to carbapenems in K. pneumoniae is increasing dramatically in Chinese hospitals. Here, we report the genome sequence of NDM-1- and KPC-2-co-producing K. pneumoniae isolated from a bloodstream infection in Hangzhou, China. Methods The whole genome sequence of the strain was determined using the Illumina NovaSeq 6000 platform. Antimicrobial resistance genes were identified using the BacWGSTdb server. The phylogenetic relationship between CRKP380 and other K. pneumoniae strains isolated from Hangzhou that currently deposited in the NCBI GenBank database was analysed using the core genome single nucleotide polymorphisms strategy. Results K. pneumoniae CRKP380 was resistant to all antibiotics tested except tigecycline and colistin. The genome sequence of K. pneumoniae CRKP380 consisted of 75 contigs comprising 5,590,460 bp. According to the Pasteur MLST scheme, CRKP380 belongs to sequence type (ST) 11. Eight antimicrobial resistance genes were identified in CRKP380, including two carbapenemase genes, blaKPC-2 and blaNDM-1. Ten phylogenetically related K. pneumoniae strains from Hangzhou were identified with the identical antimicrobial resistance genes and the same capsular serotype KL105, but none of these strains carried the blaNDM gene. Conclusions In summary, we report the genome sequence of a K. pneumoniae ST11 clinical strain co-carrying blaNDM-1 and blaKPC-2 from Hangzhou, China. The genome sequence of CRKP380 can be used as a reference sequence for future comparative genomic analysis, including acquisition and mobilization of carbapenem resistance genes.