摘要
目的 评价dapb1基因对诺卡菌属系统分类和物种鉴定的能力。方法 从公共数据库中获得230株菌株(198株诺卡菌属菌株和32株非诺卡菌属菌株)基因组序列,从198株诺卡菌(90株模式菌株、31株标准菌株和77株临床菌株)基因组中提取dapb1基因,采用clustalo进行多序列比对,并用iqtree构建系统发育树。计算全基因组平均核苷酸一致性(average nucleotide identity, ANI),并对16S rRNA序列进行PCR扩增,扩增片段经纯化后测序,与dapb1基因鉴定结果进行比较。结果 基于dapb1基因对诺卡菌模式菌株构建系统发育树,90株诺卡菌模式菌株被分为5个进化分支,种间相似度为73.80%~97.74%,平均相似度为82.40%。将该方法应用于31株诺卡菌标准菌株和77株临床菌株,结果显示16S rRNA基因与ANI一致率为77.7%,而dapb1基因与ANI一致率为100%,dapb1基因比16S rRNA基因具有更高的分辨率和准确性,可对诺卡菌进行准确的定种。其98.08%的序列相似度可作为诺卡菌菌种鉴定的界值。结论 dapb1基因具有良好的种间分辨率,可对诺卡菌进行快速、准确的定种,能够真实反映诺卡菌种间的系统发育关系,可应用于诺卡菌菌群遗传结构分析、暴发溯源和流行株的传播监测。
Objective To evaluate the ability of the dapb1 gene in taxonomic classification and species identification of Nocardia. Methods The genome sequences of 230 strains(198 Nocardia strains and 32 non-Nocardia strains) were downloaded from public database, and the dapb1 genes were extracted from the genomes of 198 Nocardia strains(90 type strains, 31 reference strains and 77 clinical strains). Multi sequence alignment was conducted with clustalo, and the phylogenetic trees were constructed by using iqtree. The average nucleotide identity(ANI) was calculated, and the 16 S rRNA sequence was amplified by PCR, and the amplified fragment was purified and sequenced and compared with the identification result of the dapb1 gene. Results Based on the dapb1 gene, a phylogenetic tree of type strains of Nocardia was constructed,90 type strains were divided into five clades. The sequence similarity of the dapb1 gene among species was 73.80%–97.74%,and the average similarity was 82.40%. This method was applied for 31 reference strains and 77 clinical strains of Nocardia.The result showed that the concordance rate between 16 S rRNA gene and ANI was 77.7%, while the concordance rate between the dapb1 gene and ANI was 100%. Using dapb1 gene has higher resolution ratio and accuracy than using 16 S rRNA gene to accurately identify Nocardia species. The sequence similarity of 98.08% can be used as a cut-off value for the species identification of Nocardia. Conclusion Using dapb1 gene has a good interspecies resolution ratio to quickly and accurately identify Nocardia species and truly reflect the phylogenetic relationship among Nocardia species, which can be widely applied in the analysis on genetic structure of Nocardia, outbreak tracing, and surveillance for circulating strains.
作者
徐帅
车彦林
李臻鹏
黄元铭
韩李超
李丹
李振军
Xu Shuai;Che Yanlin;Li Zhenpeng;Huang Yuanming;Han Lichao;Li Dan;Li Zhenjun(State Key Laboratory for Infectious Disease Prevention and Control,National Institute for Communicable Disease Control and Prevention,Chinese Center for Disease Control and Prevention,Beijing 102206,China;Key Laboratory of Laboratory Medicine,Ministry of Education of China,Wenzhou Medical University,Wenzhou 325035,Zhejiang,China)
出处
《疾病监测》
CAS
CSCD
北大核心
2022年第2期191-197,共7页
Disease Surveillance
基金
生物安全重点专项课题(No.2019YFC1200700,No.2019YFC1200601)
国家自然科学基金(No.82073624)。
关键词
诺卡菌
dapb1基因
系统分类
细菌鉴定
Nocardia
dapb1 gene
Taxonomic classification
Species identification
