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Rapid and Comprehensive Identification of Nontuberculous Mycobacteria

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Nanopore Sequencing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2632))

Abstract

Next-generation sequencing is a powerful tool to accurately identify pathogens. The MinION sequencer is best suited for the rapid identification of bacterial species due to its real-time sequence output. In this chapter, we introduce a method to identify nontuberculous mycobacteria (NTM) in one sequencing analysis from culture isolates using the MinION sequencer. NTM disease is now recognized as a growing global health concern due to its increasing incidence and prevalence. There are over 200 NTM species, of which the major pathogens are further classified into many subspecies showing different antibiotic susceptibilities. Therefore, identifying the pathogens at the subspecies level of NTM is necessary to select an appropriate treatment regimen. The protocol described here includes DNA extraction by lysis using silica beads, library preparation, sequencing by the MinION sequencer, and analysis of multilocus sequence typing using the software “mlstverse” and enables rapid and comprehensive identification of 175 species of NTM at the subspecies level with high sensitivity and accuracy.

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Author information

Authors and Affiliations

  1. Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan

    Yuki Matsumoto & Shota Nakamura

  2. Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan

    Shota Nakamura

Authors
  1. Yuki Matsumoto
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  2. Shota Nakamura
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Corresponding author

Correspondence to Shota Nakamura .

Editor information

Editors and Affiliations

  1. Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan

    Kazuharu Arakawa

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Matsumoto, Y., Nakamura, S. (2023). Rapid and Comprehensive Identification of Nontuberculous Mycobacteria. In: Arakawa, K. (eds) Nanopore Sequencing. Methods in Molecular Biology, vol 2632. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2996-3_17

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  • DOI: https://doi.org/10.1007/978-1-0716-2996-3_17

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2995-6

  • Online ISBN: 978-1-0716-2996-3

  • eBook Packages: Springer Protocols

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