Genomic and phylogenetic analysis of a NDM-1 producing ST152 Klebsiella pneumoniae isolated from a bloodstream infection in China

Renchi Fang; Lingfang Di; Xuebin Tian; Yongfeng Bai

doi:10.1016/j.jgar.2024.11.005

Genomic and phylogenetic analysis of a NDM-1 producing ST152 Klebsiella pneumoniae isolated from a bloodstream infection in China

J Glob Antimicrob Resist. 2024 Nov 27:40:34-36. doi: 10.1016/j.jgar.2024.11.005. Online ahead of print.

Authors

Renchi Fang¹, Lingfang Di², Xuebin Tian³, Yongfeng Bai⁴

Affiliations

¹ Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang Key Laboratory of Clinical In Vitro Diagnostic Techniques, Hangzhou, China; Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China.
² Department of Clinical Laboratory, Tongxiang First people's hospital, Tongxiang, China.
³ State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
⁴ Department of Clinical Laboratory, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China. Electronic address: [email protected].

PMID: 39608707
DOI: 10.1016/j.jgar.2024.11.005

Abstract

Purpose: The aim of this study was to characterize the genomic structure of the first isolated ST152 Klebsiella pneumoniae strain carrying bla_NDM-1 in China.

Methods: Antimicrobial susceptibility was determined by broth microdilution method. Whole-genome sequencing was conducted using the Illumina HiSeq and Oxford Nanopore GridION X5 platforms, and the genomic features were analyzed using a range of bioinformatics tools.

Results: The strain HZKP1 demonstrated resistance to cefepime, ceftazidime, amoxicillin-clavulanic acid, amikacin, ciprofloxacin, meropenem, imipenem, and ertapenem, while showing sensitivity to tigecycline and colistin. It was classified as sequence type (ST) 152, K locus (KL) 105 and OC locus (OCL) O3b, respectively. The bla_NDM-1 gene was identified on the IncX3 plasmid pHZKP1-NDM (54,035 bp), located downstream of the ISKox3-IS3000-ISAba125-IS5 segment and upstream of the ble_MBL-IS26-bla_SHV-69-IS26 segment. Phylogenetic analysis indicated its closest relative to be a strain isolated from a wound swab sample in Tanzania in 2013, differing by 598 alleles.

Conclusion: We characterized genomic features of the first ST152 K. pneumoniae strain isolated in China. Our findings provide insights into the current status of resistance in new lineages within the region and enhance comprehension of K. pneumoniae carbapenem resistance transmission from a genetic structure perspective.

Keywords: Klebsiella pneumoniae; ST152; Whole genome sequencing; bla(NDM-1).