| 全基因组测序在病原菌分型与溯源中的应用研究进展 |
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| 引用本文： | 贾慧琼,阮陟. 全基因组测序在病原菌分型与溯源中的应用研究进展[J]. 微生物学报, 2022, 62(3): 949-967 |
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| 作者姓名： | 贾慧琼 阮陟 |
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| 作者单位： | 浙江大学医学院附属第一医院检验科, 浙江 杭州 310003;浙江省临床体外诊断技术研究重点实验室, 浙江 杭州 310003;浙江大学医学院附属邵逸夫医院生物医学研究中心, 浙江 杭州 310016;浙江省微生物技术与生物信息研究重点实验室, 浙江 杭州 310016 |
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| 基金项目： | 国家自然科学基金（82102436，81401698）；浙江省自然科学基金（LY21H190001）；浙江省公益技术研究计划（LGF18H190001） |
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| 摘 要： | 细菌分子分型已成为监测细菌感染性疾病的暴发流行与明确病原菌传播途径的重要工具.随着全基因组测序技术的日益兴起,公共数据库中已产生大量的细菌基因组数据,迫切需要研究人员充分认识和理解该技术,并掌握多种生物信息学工具挖掘并解读测序数据.本文系统概述了全基因组测序技术与生物信息学工具在病原菌分型与溯源中的应用,并对全基因组测...
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| 关 键 词： | 全基因组测序 生物信息学 基因组流行病学 分型与溯源 暴发流行 |
| 收稿时间： | 2021-01-05 |
| 修稿时间： | 2021-10-07 |
Advances on whole genome sequencing-powered typing and source tracking of bacterial pathogens |
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| JIA Huiqiong,RUAN Zhi. Advances on whole genome sequencing-powered typing and source tracking of bacterial pathogens[J]. Acta microbiologica Sinica, 2022, 62(3): 949-967 |
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| Authors: | JIA Huiqiong RUAN Zhi |
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| Affiliation: | Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University, Hangzhou 310003, Zhejiang, China;Key Laboratory of Clinical In vitro Diagnostic Techniques of Zhejiang Province, Hangzhou 310003, Zhejiang, China; Department of Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China;Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310016, Zhejiang, China |
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| Abstract: | Molecular typing has been an important technique to monitor the outbreak of bacterial infections and the transmission routes of bacterial pathogens. Improvements in the next-generation sequencing technologies are facilitating rapid and cost-effective molecular diagnosis and genotyping in identification, characterization, and source tracking of bacterial pathogens. With the advancement of microbial whole genome sequencing techniques, a large volume of bacterial genome data have been produced and deposited in public databases, which necessitate the need of a variety of bioinformatics tools to analyze and interpret these data. This review provided an overview of the whole genome sequencing-powered typing and source tracking of bacterial pathogens by various cutting-edge bioinformatics tools. We also discussed the bottleneck in the deployment of this technology in clinical practice and the future application prospects in bacterial infectious disease management. |
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| Keywords: | whole genome sequencing bioinformatics genomic epidemiology typing and source tracking outbreak |
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