Unravelling the genome sequence of a pandrug-resistant Klebsiella pneumoniae isolate with sequence type 11 and capsular serotype KL64 from China.

Abstract

Klebsiella pneumoniae has emerged worldwide as a major cause of severe infections owing to the rising prevalence of multidrug-resistant strains in clinical settings. This study aimed to investigate the genomic features of pandrug-resistant K. pneumoniae strain KP2 with high colistin and tigecycline resistance isolated from a patient in China. The antimicrobial susceptibility of K. pneumoniae KP2 was determined by microdilution broth assay. Whole genomic DNA was extracted and was sequenced using an Illumina HiSeq X10 platform. De novo genome assembly was performed using Unicycler, and the draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). The sequence type (ST), capsular type, antimicrobial resistance and virulence-related genes were identified from the genome sequence. Core genome multilocus sequence typing (cgMLST) analysis was performed by BacWGSTdb server. Klebsiella pneumoniae KP2 was resistant to all antimicrobial agents tested, including colistin and tigecycline. The genome size was calculated as 5 729 339bp, with 5772 protein-coding sequences and a G+C content of 57.0%. The isolate was assigned to ST11 with capsular serotype KL64. Several antimicrobial resistance genes and virulence genes as well as genomic islands and multiple insertion sequences were identified in the genome sequence. The closest relative of K. pneumoniae KP2 was another isolate from Hangzhou that differed by only 45 cgMLST loci. The genome sequence data presented in this study can serve as an important reference sequence for further understanding of the antimicrobial resistance mechanisms and virulence potential of this bacterial species.