A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer.
A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer.
复制标题
DOI：
10.1038/s41598-017-05772-5
复制
发表时间：
2017-07-18
影响因子：
4.6
通讯作者：
Imanishi T
中科院分区：
文献类型：
--
作者：
Mitsuhashi S;Kryukov K;Nakagawa S;Takeuchi JS;Shiraishi Y;Asano K;Imanishi T
我们开发了一种用于16 S rDNA分析的便携式系统，该系统由基于纳米孔技术的测序仪、MinION和笔记本电脑组成，并评估了其快速确定细菌组成的潜在能力。我们使用含有等摩尔16S rDNA的模拟细菌群落和来自脓胸患者的胸腔积液测试了我们的方案的时间有效性和准确性。靶向16S rDNA的MinION测序检测了模拟细菌群落中存在的所有20种细菌。时程分析表明，在测序的前5分钟期间获得的序列数据（1，379个细菌读数）足以检测模拟样品中的所有20种细菌并确定物种组成，与从4小时测序获得的结果（24，202个读数）一致。此外，使用从脓胸患者胸腔积液中提取的临床样本，我们可以使用我们的快速测序和分析方案来识别胸腔积液中的主要细菌病原体。所有结果与使用IonPGM测序仪的常规16S rDNA测序结果相当。我们的研究结果表明，快速测序和细菌组成的测定是可能的，在获得DNA样品后2小时内。
We developed a portable system for 16S rDNA analyses consisting of a nanopore technology-based sequencer, the MinION, and laptop computers, and assessed its potential ability to determine bacterial compositions rapidly. We tested our protocols using a mock bacterial community that contained equimolar 16S rDNA and a pleural effusion from a patient with empyema, for time effectiveness and accuracy. MinION sequencing targeting 16S rDNA detected all 20 of the bacterial species present in the mock bacterial community. Time course analysis indicated that the sequence data obtained during the first 5 minutes of sequencing (1,379 bacterial reads) were enough to detect all 20 bacteria in the mock sample and to determine species composition, consistent with results of those obtained from 4 hours of sequencing (24,202 reads). Additionally, using a clinical sample extracted from the empyema patient’s pleural effusion, we could identify major bacterial pathogens in that effusion using our rapid sequencing and analysis protocol. All results are comparable to conventional 16S rDNA sequencing results using an IonPGM sequencer. Our results suggest that rapid sequencing and bacterial composition determination are possible within 2 hours after obtaining a DNA sample.
登录
查看更多内容
影响因子：
14.9
作者：
Klindworth A;Pruesse E;Schweer T;Peplies J;Quast C;Horn M;Glöckner FO
通讯作者：
Glöckner FO
影响因子：
12.3
作者：
Grumaz S;Stevens P;Grumaz C;Decker SO;Weigand MA;Hofer S;Brenner T;von Haeseler A;Sohn K
通讯作者：
Sohn K
影响因子：
7
作者：
Kielbasa, Szymon M.;Wan, Raymond;Frith, Martin C.
通讯作者：
Frith, Martin C.
影响因子：
12.3
作者：
Jain M;Olsen HE;Paten B;Akeson M
通讯作者：
Akeson M
影响因子：
6.4
作者：
Pearce MM;Hilt EE;Rosenfeld AB;Zilliox MJ;Thomas-White K;Fok C;Kliethermes S;Schreckenberger PC;Brubaker L;Gai X;Wolfe AJ
通讯作者：
Wolfe AJ