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

替代計量分析
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其它資訊
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.
著者Cheung M.K., Kwan H.S.
期刊名稱Public Health Genomics
出版年份2012
月份11
日期1
卷號15
期次6
出版社S. Karger AG
出版地Switzerland
頁次341 - 351
國際標準期刊號1662-4246
語言英式英語
關鍵詞Bioinformatics, Epidemiology, Next-generation, NGS, Outbreak genomics, Sequencing

上次更新時間 2020-26-11 於 02:30