Main menu

Rapid sequencing‐based diagnosis of infectious bacterial species from meningitis patients in Zambia


Objectives
We have developed a portable system for the rapid determination of bacterial composition for the diagnosis of infectious diseases. Our system comprises of a nanopore technology‐based sequencer, MinION, and two laptop computers. To examine the accuracy and time efficiency of our system, we provided a proof‐of‐concept for the detection of the causative bacteria of 11 meningitis patients in Zambia.

Methods
We extracted DNA from cerebrospinal fluid samples of each patient and amplified the 16S rRNA gene regions. The sequencing library was prepared, and the sequenced reads were simultaneously processed for bacterial composition determination using the minimap2 software and the representative prokaryote genomes.

Results
The sequencing results of four of the six culture‐positive samples were consistent with those of conventional culture‐based methods. The dominant bacterial species in each of these samples were identified from the sequencing data within only 3 min. Although the major bacterial species were also detected from the other two culture‐positive samples and five culture‐negative samples, their presence could not be confirmed. Moreover, as a whole, although the number of sequencing reads obtained within a short sequencing run was small, there was no change in the major bacterial species over time with prolonged sequencing. In addition, the processing time strongly correlated with the number of sequencing reads used for the analysis.

Conclusion
Our results suggest that time‐effective analysis could be achieved by determining the number of sequencing reads required for the rapid diagnosis of infectious bacterial species depending on the complexity of bacterial species in a sample.

Authors: So Nakagawa, Shigeaki Inoue, Kirill Kryukov, Junya Yamagishi, Ayumu Ohno, Kyoko Hayashida, Ruth Nakazwe, Mox Kalumbi, Darlington Mwenya, Nana Asami, Chihiro Sugimoto, Mable M Mutengo, Tadashi Imanishi

入门指南

购买 MinION 启动包 Nanopore 商城 测序服务提供商 全球代理商

联系我们

Intellectual property Cookie policy Corporate reporting Privacy policy Terms & conditions Accessibility

关于 Oxford Nanopore

Contact us 领导团队 媒体资源和联系方式 投资者 在 Oxford Nanopore 工作 BSI 27001 accreditationBSI 90001 accreditationBSI mark of trust
Chinese flag