Nov 12, 2019

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

Clinical & Translational Immunology
So NakagawaTadashi Imanishi


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. 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. 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, ther...Continue Reading

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Mentioned in this Paper

Computer Software
Protein Sequence Determination
Run-On Assays
Determination Aspects
Nucleic Acid Sequencing
Cerebrospinal Fluid
Laboratory Culture

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