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

IF 3.2 3区医学 Q2 INFECTIOUS DISEASES Journal of global antimicrobial resistance Pub Date : 2025-01-01 DOI:10.1016/j.jgar.2024.11.005

Renchi Fang , Lingfang Di , Xuebin Tian , Yongfeng Bai

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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.

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一株产NDM-1的ST152肺炎克雷伯菌的基因组和系统发育分析

目的：研究中国首次分离到的携带blaNDM-1的ST152肺炎克雷伯菌的基因组结构。方法：采用微量肉汤稀释法测定药敏。使用Illumina HiSeq和Oxford Nanopore MinION平台进行全基因组测序，并使用一系列生物信息学工具分析基因组特征。结果：菌株HZKP1对头孢吡肟、头孢他啶、阿莫西林-克拉维酸、阿米卡星、环丙沙星、美罗培南、亚胺培南、厄他培南耐药，对替加环素、粘菌素敏感。序列型（ST） 152， K位点（KL） 105， OC位点（OCL） O3b。blaNDM-1基因位于IncX3质粒pHZKP1-NDM （54,035 bp）上，位于ISKox3-IS3000-ISAba125-IS5片段的下游和blemll - is26 - blashv -69- is26片段的上游。系统发育分析表明，其最近的近亲是2013年从坦桑尼亚伤口拭子样本中分离出来的菌株，存在598个等位基因差异。结论：初步鉴定了中国首例分离到的ST152肺炎克雷伯菌的基因组特征。我们的研究结果为该地区新谱系的耐药现状提供了见解，并从遗传结构的角度增强了对肺炎克雷伯菌碳青霉烯类耐药传播的理解。

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来源期刊

Journal of global antimicrobial resistance INFECTIOUS DISEASES-PHARMACOLOGY & PHARMACY

CiteScore

8.70

自引率

2.20%

发文量

285

审稿时长

34 weeks

期刊介绍： The Journal of Global Antimicrobial Resistance (JGAR) is a quarterly online journal run by an international Editorial Board that focuses on the global spread of antibiotic-resistant microbes. JGAR is a dedicated journal for all professionals working in research, health care, the environment and animal infection control, aiming to track the resistance threat worldwide and provides a single voice devoted to antimicrobial resistance (AMR). Featuring peer-reviewed and up to date research articles, reviews, short notes and hot topics JGAR covers the key topics related to antibacterial, antiviral, antifungal and antiparasitic resistance.