Application of highly portable MinION nanopore sequencing technology for the monitoring of nosocomial tuberculosis infection.
Application of highly portable MinION nanopore sequencing technology for the monitoring of nosocomial tuberculosis infection.
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DOI：
10.1016/j.ijmyco.2016.10.035
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发表时间：
2016-12-01
影响因子：
1.2
通讯作者：
O'Grady, Justin
中科院分区：
文献类型：
--
作者：
Bates, Matthew;Polepole, Pascal;O'Grady, Justin
撒哈拉以南非洲的转诊医院集中了大量结核病和耐多药结核病患者，这些患者在社区结核病服务中失败了。我们以前通过加强筛查和尸检研究表明，赞比亚卢萨卡大学教学医院漏诊结核感染的负担很大，许多患者死亡或未经治疗就出院。由于结核病隔离设施极少，投资于更广泛的筛查和隔离的政治意愿也极少，医院传播的风险可能极高。来自其他低负担医院和南非的研究表明，下一代测序（NGS）是一种非常强大的工具，可用于快速测序整个结核病基因组并进行比较，以确认或排除医院传播。已建立的NGS分析平台，如Illumina，非常昂贵，固定，需要定期维护，使其成为非洲研究提案或计划干预赠款的昂贵内容。MinION纳米孔测序通过廉价的便携式测序仪、快速简单的文库制备（15分钟）和自动化实时分析工具改变了NGS的格局。高度便携的MinION纳米孔测序技术在医院结核感染监测中的应用将被讨论。我们的儿科肺炎研究的初步数据将证明在大学教学医院收治的儿童的诱导痰中检测到结核病。
Referral hospitals in sub-Saharan Africa concentrate large numbers of tuberculosis (TB) and multidrug-resistant TB (MDR-TB) patients, failed by community TB services. We have previously shown, from enhanced screening and through autopsy studies, a significant burden of missed TB infections at the University Teaching Hospital, Lusaka, Zambia, with many patients dying or being discharged without treatment. With minimal TB isolation facilities and minimal political will to invest in broader screening and isolation, the risk of nosocomial transmission is likely to be extremely high. Studies from other hospitals in low burden settings and in South Africa have shown that next generation sequencing (NGS) is a very powerful tool for rapidly sequencing whole TB genomes and comparing them to confirm or rule out nosocomial transmission. The established platforms for NGS analysis, such as Illumina, are very expensive, immobile, and require regular maintenance, making them a costly inclusion on a research proposal or programmatic intervention grant in Africa. MinION nanopore sequencing has changed the NGS landscape with cheap portable sequencers, rapid simple library preparation (15min), and automated real-time analysis tools. The application of highly portable MinION nanopore sequencing technology for the monitoring of nosocomial TB infection will be discussed. Preliminary data from our pediatric pneumonia study will demonstrate the detection of TB in induced sputum from children admitted to the University Teaching Hospital.