Hybrid Genome Assembly and Annotation of a Pandrug-Resistant Klebsiella pneumoniae Strain Using Nanopore and Illumina Sequencing
Hybrid Genome Assembly and Annotation of a Pandrug-Resistant Klebsiella pneumoniae Strain Using Nanopore and Illumina Sequencing
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使用 Nanopore 和 Illumina 测序对全耐药肺炎克雷伯菌菌株进行混合基因组组装和注释
DOI：
10.2147/idr.s240404
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发表时间：
2020-01-01
影响因子：
3.9
通讯作者：
He, Fang
中科院分区：
文献类型：
--
作者：
Ruan, Zhi;Wu, Jianyong;He, Fang
背景：耐多药肺炎克雷伯菌在世界范围内的流行越来越多地与各种高死亡率的感染有关。在这里，我们报道了肺炎克雷伯菌KP58株的全基因组序列，该株肺炎克雷伯菌对粘菌素和替格环素表现出高水平的耐药性。方法从杭州某三级医院住院的女性患者中国的尿样中分离到肺炎克雷伯菌KP58。进行药敏试验，测定最低抑菌浓度(MIC)。使用Illumina和牛津纳米孔测序技术进行全基因组测序。利用多种生物信息学方法对其基因组特征、抗菌素抗性基因和毒力基因进行了综合分析。此外，利用在线细菌全基因组序列分型和来源追踪数据库BacWGSTdb中的核心基因组多位点序列分型(CgMLST)分析，对肺炎克雷伯菌KP58及其近缘分离株进行了基因组流行病学和系统发育分析。结果肺炎克雷伯菌KP58对包括替吉环素和粘菌素在内的所有抗菌药物均耐药。将这两种测序技术相结合，可以获得高质量的肺炎克雷伯菌KP58全基因组序列，其中包括1条环状染色体和5个环状质粒。该菌株具有多种获得性抗菌素耐药性和毒力决定因素。它还在中断的mgrB基因上带有一个类似ISKpn26的插入，这赋予了粘菌素抗性。替格环素耐药与AcrAB外排系统的过度表达有关。与肺炎克雷伯菌KP58最近的亲缘关系是从杭州分离到的另一株临床分离株，只有10个cgMLST基因座的差异。结论本研究提供的数据集为医院耐药肺炎克雷伯菌的演变提供了重要的洞察力，并有助于制定有效的控制策略。采取适当的监测和控制措施对防止其进一步传播至关重要。
Background The prevalence of multidrug-resistant Klebsiella pneumoniae is increasingly being implicated worldwide in a variety of infections with high mortalities. Here, we report the complete genome sequence of K. pneumoniae strain KP58, a pandrug-resistant K. pneumoniae strain that exhibits high levels of resistance to colistin and tigecycline in China. Methods The K. pneumoniae strain KP58 was recovered from a urine sample of a female patient hospitalized in a tertiary hospital in Hangzhou, China. Antimicrobial susceptibility testing was performed and the minimum inhibitory concentrations (MICs) were determined. Whole-genome sequencing was performed using Illumina and Oxford nanopore sequencing technologies. Genomic features, antimicrobial resistance genes and virulence genes were comprehensively analysed by various bioinformatics approaches. In addition, genomic epidemiological and phylogenetic analyses of K. pneumoniae KP58 and closely related isolates were performed using the core genome multilocus sequence typing (cgMLST) analysis in BacWGSTdb, an online bacterial whole-genome sequence typing and source tracking database. Results K. pneumoniae KP58 was resistant to all antimicrobial agents tested, including tigecycline and colistin. Combining the two sequencing technologies allowed a high-quality complete genome sequence of K. pneumoniae KP58 comprising one circular chromosome and five circular plasmids to be obtained. This strain harbours a variety of acquired antimicrobial resistance and virulence determinants. It also carried an ISKpn26-like insertion in the disrupted mgrB gene, which confers colistin resistance. The tigecycline resistance was associated with overexpression of the AcrAB efflux system. The closest relative of K. pneumoniae KP58 was another clinical isolate recovered from Hangzhou that differed by only 10 cgMLST loci. Conclusion The dataset presented in this study provides essential insights into the evolution of antimicrobial-resistant K. pneumoniae in hospital settings and assists in the development of effective control strategies. Appropriate surveillance and control measures are essential to prevent its further dissemination.