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

Abstract

OBJECTIVES\nKlebsiella 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 a pandrug-resistant K. pneumoniae KP2 with high colistin and tigecycline resistance recovered from a patient in China.\n\n\nMETHODS\nAntimicrobial susceptibility of K. pneumoniae KP2 was determined by the microdilution broth assay. Whole genomic DNA was extracted and sequenced using the Illumina HiSeq 4000 platform. De novo genome assembly was performed using Unicycler and the draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline. The sequence type (ST), capsular type, antimicrobial resistance and virulence-related genes were identified from the genome sequence. The core genome multilocus sequence typing (cgMLST) analysis was performed by BacWGSTdb server.\n\n\nRESULTS\nThe K. pneumoniae KP2 was resistant to all antimirobial agents tested including colistin and tigecycline. The genome size was calculated as 5,729,339 bp, with 5,772 protein-coding sequences and GC content of 57.0%. This isolate was assigned to sequence type ST11 with the capsular serotype as KL64. Several antimicrobial resistance genes and the 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 Hangzhou isolate, differed by only 45 cgMLST loci.\n\n\nCONCLUSION\nThe genome sequence data presented in this study can serve as an important reference sequence for further understanding of the antimicrobial resistance mechanisms and virulence potientials of this bacterial species.