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A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer.

Satomi Mitsuhashi1, Kirill Kryukov1, So Nakagawa1

  • 1Biomedical Informatics Laboratory, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan.

Scientific Reports
|July 20, 2017
PubMed
Summary

This study introduces a portable nanopore sequencing system for rapid bacterial identification using 16S rDNA analysis. The system accurately determines bacterial composition from mock and clinical samples in under two hours.

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • 16S ribosomal DNA (rDNA) sequencing is crucial for bacterial identification.
  • Rapid and accurate bacterial composition analysis is needed in clinical settings.
  • Portable sequencing technologies offer potential for point-of-care diagnostics.

Purpose of the Study:

  • To develop and evaluate a portable system for rapid 16S rDNA-based bacterial analysis.
  • To assess the time-effectiveness and accuracy of nanopore sequencing for bacterial identification.
  • To compare nanopore sequencing results with conventional methods.

Main Methods:

  • Development of a portable system using a MinION nanopore sequencer and laptop computers.
  • Testing with a mock bacterial community and a clinical pleural effusion sample.
  • Time-course analysis of sequencing data for bacterial detection and composition determination.
  • Comparison of results with conventional 16S rDNA sequencing on an IonPGM platform.

Main Results:

  • The portable system successfully detected all 20 bacterial species in the mock community.
  • Accurate species composition was determined within the first 5 minutes of sequencing.
  • Major bacterial pathogens were identified in a clinical empyema sample.
  • Results were comparable to conventional sequencing methods.

Conclusions:

  • A portable nanopore sequencing system enables rapid and accurate bacterial composition analysis.
  • Bacterial identification and composition determination are feasible within 2 hours of DNA extraction.
  • This technology holds promise for timely clinical diagnostics and microbial research.