中国县级医院发现的耐碳青霉烯类肺炎克雷伯菌共携带 blaNDM-5 和 blaKPC-2 胶囊型 KL25 的基因组特征

IF 2.9 3区医学 Q2 INFECTIOUS DISEASES

Infection and Drug Resistance Pub Date : 2024-09-14 DOI:10.2147/idr.s479560

Yuanzhong Fang, Juan Jin, Minfei Peng, Lidong Xu, Linyuan Gu, Danni Bao, Qiuying Zhang, Kainan Jin

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引用次数: 0

摘要

背景：耐高毒性碳青霉烯类耐药肺炎克菌（hv-CRKP）已在全球范围内迅速蔓延。在此，我们研究了中国某县级医院分离的ST11肺炎克菌SM117的基因组特征，该菌具有荚膜血清型KL25，同时携带blaNDM-5、两个拷贝的blaKPC-2和多个质粒携带的毒力基因：方法：评估了肺炎克雷伯菌 SM117 的抗菌药敏感性。采用 Illumina NovaSeq 6000 和 Oxford Nanopore MinION 平台对基因组进行测序，然后进行从头组装。利用 NCBI 原核基因组注释管道对基因组序列进行注释，并进一步鉴定序列类型（ST）、囊型、抗生素耐药基因、质粒复制子类型和毒力基因。利用 CSI Phylogeny 1.4 根据核心基因组单核苷酸多态性（cgSNPs）进行了系统发育分析，并通过交互式生命树（iTOL）V5 网络服务器进一步实现了可视化：结果：肺炎双球菌 SM117 的全基因组序列由 8 个等位基因组成，总长度为 6,104,486 bp，包含一个 5,612,620 bp 的单染色体和 7 个质粒。该分离株被归入 ST11，具有荚膜血清型 KL25，同时携带 blaNDM-5、blaKPC-2 和多个质粒携带的毒力基因，包括 rmpA2 和气单胞菌素基因 iucABCD-iutA。肺炎克雷伯菌株中同时存在的 blaKPC 和 blaNDM 表现出对β-内酰胺类抗生素的高度耐药性。菌株 SM117 也携带多种抗生素耐药基因，使其对除多粘菌素以外的所有抗生素都具有耐药性。2023 年，从中国浙江的医院体表样本中发现了肺炎克氏菌 C793 的近亲，其 SNPs 仅相差 52 个：本研究报告了中国耐多药 ST11 肺炎克菌的基因组特征，该菌具有荚膜血清型 KL25，同时携带 blaNDM-5、两个 blaKPC-2 基因拷贝和多个质粒携带的毒力基因。这些发现将为了解耐多药肺炎克氏菌的抗生素耐药机制、基因组流行病学特征和传播动态提供重要信息。

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Genomic Characteristics of a Carbapenem-Resistant Klebsiella pneumoniae Co-Carrying blaNDM-5 and blaKPC-2 Capsular Type KL25 Recovered from a County Level Hospital in China

Background: Hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP) has been spreading rapidly worldwide. Here, we investigated the genomic characteristics of ST11 K. pneumoniae isolate SM117 with capsular serotype KL25, co-carrying bla_NDM-5, two copies of bla_KPC-2 and multiple plasmid-borne virulence genes from a county level hospital in China.
Methods: Antimicrobial susceptibility of K. pneumoniae SM117 was evaluated. The Illumina NovaSeq 6000 and Oxford Nanopore MinION platforms were applied to sequence the genome and then de novo assembled. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline and further subjected to identify the sequence type (ST), capsular type, antibiotic resistance genes, plasmid replicon types and virulence genes. The phylogenetic analysis was performed based on the core genome single nucleotide polymorphisms (cgSNPs) using CSI Phylogeny 1.4, and further visualized by Interactive Tree of Life (iTOL) V5 web server.
Results: The whole-genome sequence of K. pneumoniae SM117 is made up of eight contigs totaling 6,104,486 bp, contain a 5,612,620 bp single chromosome and seven plasmids. The isolate was assigned to ST11 with capsular serotype KL25, co-carrying including bla_NDM-5, bla_KPC-2 and multiple plasmid-borne virulence genes including rmpA2 and aerobactin genes iucABCD-iutA. The coexistence of bla_KPC and bla_NDM in K. pneumoniae strains exhibit a high degree of resistance to β-lactam antibiotics. The strain SM117 also carries multiple antibiotic resistance genes, making it resistant to all antibiotics except polymyxin. The closest relative of K. pneumoniae C793 was identified in 2023 from a hospital surface sample in Zhejiang, China, with just 52 SNPs difference.
Conclusion: This study reported the genomic characteristics of a multidrug-resistant ST11 K. pneumoniae with capsular serotype KL25, co-carrying bla_NDM-5, two copies of bla_KPC-2 genes and multiple plasmid-borne virulence genes in China. These findings will provide important knowledge of the antibiotic resistance mechanisms, genomic epidemiological characteristics and transmission dynamics of multidrug-resistant K. pneumoniae.

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来源期刊

Infection and Drug Resistance Medicine-Pharmacology (medical)

CiteScore

5.60

自引率

7.70%

发文量

826

审稿时长

16 weeks

期刊介绍： About Journal Editors Peer Reviewers Articles Article Publishing Charges Aims and Scope Call For Papers ISSN: 1178-6973 Editor-in-Chief: Professor Suresh Antony An international, peer-reviewed, open access journal that focuses on the optimal treatment of infection (bacterial, fungal and viral) and the development and institution of preventative strategies to minimize the development and spread of resistance.