Fighting outbreaks with bacterial genomics: Case review and workflow proposal
Publication in refereed journal


香港中文大学研究人员 ( 现职)

关海山教授 (生命科学学院)

张文杰先生 (食品研究中心)

全文

数位物件识别号 (DOI) http://dx.doi.org/10.1159/000342770

引用次数
Web of Sciencehttp://aims.cuhk.edu.hk/converis/portal/Publication/5WOS source URL
Scopushttp://aims.cuhk.edu.hk/converis/portal/Publication/5Scopus source URL

其它资讯

摘要Background: Disease outbreak investigation is a key aspect of public health. Whole-genome sequencing of bacterial pathogen based on new generation high-throughput sequencing technologies has facilitated outbreak investigations recently. Whilst the approach has become more affordable and accessible to research and clinical laboratories, a system for adequate and efficient analyses of genome data in the context of bacterial outbreak investigations is missing. Methods: We performed a literature review of timely genomic investigations performed during the course of bacterial outbreaks that are based on new generation sequencing technologies. Currently available bioinformatics tools for genomic analyses are also reviewed here. Results: Genomic investigations in early stages of bacterial outbreaks have shown to provide timely information on evolutionary origin, transmission route, pathogenic potential, and resistance information of the outbreak strains and allow development of strain-specific typing methods. A systematic genomic analytical workflow is proposed here for the first time to facilitate efficient extraction of epidemiologically useful information from genome data of bacterial pathogens in future bacterial outbreak investigations. Conclusion: With the continuous reduction of genome sequencing cost and development of user-friendly analytical tools, it is expected that high-throughput genome sequencing will be applied routinely for timely genomic analysis in bacterial outbreaks in the near future. Copyright ? 2012 S. Karger AG, Basel.

着者Cheung M.K., Kwan H.S.
期刊名称Public Health Genomics
出版年份2012
月份11
日期1
卷号1http://aims.cuhk.edu.hk/converis/portal/Publication/5
期次6
出版社S. Karger AG
出版地Switzerland
页次341 - 3http://aims.cuhk.edu.hk/converis/portal/Publication/51
国际标準期刊号1662-4246
语言英式英语

关键词Bioinformatics, Epidemiology, Next-generation, NGS, Outbreak genomics, Sequencing