Genome sequence of a sequence type 1 NDM-5-producing carbapenem-resistant Klebsiella pneumoniae in China

Abstract

Objectives

The emergence of carbapenem-resistant Klebsiella pneumoniae presents significant health challenges. Here, we present the structural genome sequence of an NDM-5–producing K. pneumoniae (HZKP2) in China.

Methods

Antimicrobial susceptibility tests were conducted via broth microdilution. Whole-genome sequencing was performed for genomic analysis. Wzi and capsular polysaccharide (KL) were analysed using Kaptive. Resistance genes, virulence factors, and comparative genomics analyses were also conducted. Multilocus sequence typing (MLST), replicons type, and core genome MLST analysis were further conducted using BacWGSTdb server.

Results

HZKP2 was resistant to cefepime, ceftazidime, ciprofloxacin, ciprofloxacin, meropenem, and ertapenem. It harboured fosA, bla_SHV-187, oqxA, oqxB, sul1, dfrA1, tet(A), floR, aph(6)-Id, aph(3′')-Ib, sul2, bla_CTX-M-55, and bla_NDM-5. Based on the RAST results, 5563 genes that belonged to 398 subsystems were annotated. The complete genome sequence of HZKP2 was characterized as ST1, wzi 19, and KL19, 5 five contigs totalling 5 654 446 bp, including one chromosome and four plasmids. Further analysis found that bla_NDM-5 was located in a 46 161 bp IncX3 plasmid (pHZKP2-3). The genetic structure of bla_NDM-5 gene was ISKox3-IS26-ble_MBL-bla_NDM-5-IS5-ISAb125-IS3000. Further analysis revealed that insertion sequences mediated the dissemination of bla_NDM-5 from other species of Enterobacterales. Phylogenetic analysis showed that the closest relative was from a human stool specimen in China, which differed by 53 core genome MLST alleles.

Conclusions

Our study provides the first structural perspective of the ST1 K. pneumoniae isolate producing NDM-5 in China. These results could provide valuable insights into the genetic characteristics, antimicrobial resistance mechanisms, and transmission dynamics of carbapenem-resistant K. pneumoniae in clinical settings.