He Xianhong, Xu Liwei, Dai Hangdong, Ge Minxia, Zhu Jufang, Fu Hangyu, Zhu Shuilong, Shao Jiayu
Department of Clinical Laboratory, The Third People's Hospital of Xiaoshan, Hangzhou, People's Republic of China.
Infect Drug Resist. 2023 Jun 3;16:3535-3540. doi: 10.2147/IDR.S415846. eCollection 2023.
The transmission of carbapenem-resistant Enterobacterales pose a significant threat to global public health, which weakens the effectiveness of most antimicrobial agents. The aim of this study is to present the genomic characteristics of a multidrug-resistant , which contains both and genes, discovered from a respiratory infection in China.
The antimicrobial susceptibility of isolate 488 was measured by using the broth microdilution method. The Oxford Nanopore MinION and Illumina NovaSeq 6000 platforms were applied to determine the whole-genome sequence of this isolate. De novo assembly of short Illumina reads and long MinION reads were performed by Unicycler. In silico multilocus sequence typing (MLST), antimicrobial resistance genes and plasmid replicon types were determined using the genome sequencing data. Additionally, a pairwise core genome single nucleotide polymorphism (cgSNP) comparison between 488 and all ST648 strains retrieved from NCBI GenBank database were conducted using the BacWGSTdb 2.0 server.
488 was resistant to aztreonam, levofloxacin, cefepime, fosfomycin, amikacin, imipenem, cefotaxime, and meropenem. The complete genome sequence of 488 (belong to ST648) is made up of eleven contigs totaling 5,573,915 bp, including one chromosome and ten plasmids. Eight antimicrobial resistance genes were identified, including located in a 46,161 bp IncI1-type plasmid and the gene situated in the chromosome. Other two S617-2 and R616-1 isolates, recovered from China in 2018, are the closest relatives of 488, with only 52 SNPs difference. The genome also contains at least 57 genomic islands and several IS elements.
Our study reveals the first ST648 isolate containing both and in China. These results could provide valuable insights into the genetic characteristics, antimicrobial resistance mechanisms, and transmission dynamics of carbapenem-resistant Enterobacterales in clinical settings.
耐碳青霉烯类肠杆菌科细菌的传播对全球公共卫生构成重大威胁，这削弱了大多数抗菌药物的有效性。本研究的目的是展示从中国一例呼吸道感染中发现的一株同时含有 blaNDM 和 blaOXA-48 基因的多重耐药菌的基因组特征。
采用肉汤微量稀释法测定菌株 488 的抗菌药敏性。应用牛津纳米孔 MinION 和 Illumina NovaSeq 6000 平台测定该菌株的全基因组序列。通过 Unicycler 对短的 Illumina 读段和长的 MinION 读段进行从头组装。利用基因组测序数据进行计算机多位点序列分型（MLST）、抗菌耐药基因和质粒复制子类型的测定。此外，使用 BacWGSTdb 2.0 服务器对菌株 488 与从 NCBI GenBank 数据库中检索到的所有 ST648 菌株进行成对核心基因组单核苷酸多态性（cgSNP）比较。
菌株 488 对氨曲南、左氧氟沙星、头孢吡肟、磷霉素、阿米卡星、亚胺培南、头孢噻肟和美罗培南耐药。菌株 488（属于 ST648）的完整基因组序列由 11 个重叠群组成，共 5573915 bp，包括一条染色体和 10 个质粒。鉴定出 8 个抗菌耐药基因，其中 blaNDM 位于一个 46161 bp 的 IncI1 型质粒上，blaOXA-48 基因位于染色体上。另外两株于 2018 年从中国分离出的 S617-2 和 R616-1 菌株是菌株 488 的近亲，仅相差 52 个 SNP。该基因组还包含至少 57 个基因组岛和几个插入序列元件。
我们的研究揭示了中国首例同时含有 blaNDM 和 blaOXA-48 的 ST648 菌株。这些结果可为临床环境中耐碳青霉烯类肠杆菌科细菌的遗传特征、抗菌耐药机制及传播动态提供有价值的见解。
