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Comprehensive metagenomic analysis of nontuberculous mycobacteria

Research Project

Project/Area Number 19K16643
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 49050:Bacteriology-related
Research InstitutionOsaka University

Principal Investigator

Matsumoto Yuki  大阪大学, 微生物病研究所, 特任研究員(常勤) (30749114)

Project Period (FY) 2019-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
Fiscal Year 2020: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2019: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Keywords非結核性抗酸菌症 / 病原体検出 / MLST / 全ゲノムシーケンシング / NTM
Outline of Research at the Start

非結核性抗酸菌(NTM)症の罹患率および粗死亡率は近年ともに増加傾向にあり,原因菌の同定が困難であることが治療法確立の大きな障害となっている.この要因として,NTMが環境常在菌であること,170を超える種が確認されている一方で,その多くのゲノムが未解読であることが挙げられる.本研究では,検体から直接メタゲノム解析を行う培養フリーなNTMの同定手法の開発を行うとともに,ゲノム未解読の菌種についてはゲノム解読を行い,包括的なNTMゲノムデータベースを構築する.本研究により従来6-14週間以上要していた検査は数日まで短縮されると共に,得られたゲノム配列のNTM症の治療法確立への貢献が期待される.

Outline of Final Research Achievements

The prevalence of nontuberculous mycobacteria (NTM) pulmonary diseases has been increasing worldwide. NTM consist of approximately 200 species and distinguishing between them at the subspecies level is critical to treatment. We developed a novel multi-locus sequence typing (MLST) database based on 184 genes from 7547 assemblies and an identification software, mlstverse, which can also be used for detecting other bacteria given a suitable MLST database. This method demonstrated the capacity for rapid detection of NTM, 10 min of sequencing of the ONT MinION being sufficient. Application of this methodology could improve disease epidemiology and increase the cure rates of NTM diseases.

Academic Significance and Societal Importance of the Research Achievements

NTM症は難治性の呼吸器疾患の総称であり,NTMはおよそ200種が知られ,亜種の違いにより異なる薬剤耐性を示す.そのため治療方針決定のためには亜種レベルの正確な同定が要求され,これまでの手法では正確な同定を行うことは困難であった.本研究ではこの同定を,正確かつ短期間で行う手法を確立した.これによりNTM症診断にかかる期間は従来の4-8週間から数日に短縮されるため,より早期の確定診断・治療開始が可能となり,より良い治療方法の確立へ繋がることが期待される.

Report

(4 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • 2019 Research-status Report

Research Products

(10 results)

All 2021 2020 2019 Other

All Journal Article (9 results) (of which Peer Reviewed: 7 results,  Open Access: 6 results) Remarks (1 results)

  • [Journal Article] Serum GPL core antibody levels are associated with disease activity and treatment outcomes in Mycobacterium avium complex lung disease following first line antibiotic treatment2021

    • Author(s)
      Fukushima Kiyoharu、Kitada Seigo、Matsumoto Yuki、Komukai Sho、Kuge Tomoki、Kawasaki Takahiro、Matsuki Takanori、Motooka Daisuke、Tsujino Kazuyuki、Miki Mari、Miki Keisuke、Nakamura Shota、Kida Hiroshi
    • Journal Title

      Respiratory Medicine

      Volume: 187 Pages: 106585-106585

    • DOI

      10.1016/j.rmed.2021.106585

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Pleural Effusion Caused by Mycolicibacterium mageritense in an Immunocompetent Host: A Case Report2021

    • Author(s)
      Niitsu Takayuki、Kuge Tomoki、Fukushima Kiyoharu、Matsumoto Yuki、Abe Yuko、Okamoto Masashi、Haduki Kako、Saito Haruko、Nitta Tadayoshi、Kawano Akira、Matsuki Takanori、Motooka Daisuke、Tsujino Kazuyuki、Miki Keisuke、Nakamura Shota、Kida Hiroshi、Kumanogoh Atsushi
    • Journal Title

      Frontiers in Medicine

      Volume: 8

    • DOI

      10.3389/fmed.2021.797171

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Host Immune Response and Novel Diagnostic Approach to NTM Infections2020

    • Author(s)
      Abe Yuko、Fukushima Kiyoharu、Hosono Yuki、Matsumoto Yuki、Motooka Daisuke、Ose Naoko、Nakamura Shota、Kitada Seigo、Kida Hiroshi、Kumanogoh Atsushi
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 21 Pages: 4351-4351

    • DOI

      10.3390/ijms21124351

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] The impact of adjuvant surgical treatment of nontuberculous mycobacterial pulmonary disease on prognosis and outcome2020

    • Author(s)
      Fukushima Kiyoharu、Miki Mari、Matsumoto Yuki、Uda Emi、Yamamoto Yuji、Kogita Yuya、Kagawa Yuko、Matsuki Takanori、Kagawa Hiroyuki、Oshitani Yohei、Motooka Daisuke、Tsujino Kazuyuki、Yoshimura Kenji、Miki Keisuke、Hayashi Akio、Nakamura Shota、Kitada Seigo、Takeuchi Yukiyasu、Kida Hiroshi
    • Journal Title

      Respiratory Research

      Volume: 21 Pages: 153-153

    • DOI

      10.1186/s12931-020-01420-1

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Pulmonary disease caused by a newly identified mycobacterium: Mycolicibacterium toneyamachuris: a case report2020

    • Author(s)
      Kuge Tomoki、Fukushima Kiyoharu、Matsumoto Yuki、Abe Yuko、Akiba Eri、Haduki Kako、Saito Haruko、Nitta Tadayoshi、Kawano Akira、Kawasaki Takahiro、Matsuki Takanori、Kagawa Hiroyuki、Motooka Daisuke、Tsujino Kazuyuki、Miki Mari、Miki Keisuke、Kitada Seigo、Nakamura Shota、Iida Tetsuya、Kida Hiroshi
    • Journal Title

      BMC Infectious Diseases

      Volume: 20 Pages: 888-888

    • DOI

      10.1186/s12879-020-05626-y

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population2020

    • Author(s)
      Kishikawa T, Maeda Y, Nii T, Motooka D, Matsumoto Y, Matsushita M, Matsuoka H, Yoshimura M, Kawada S, Teshigawara S, Oguro E, Okita Y, Kawamoto K, Higa S, Hirano T, Narazaki M, Ogata A, Saeki Y, Nakamura S, Inohara H, Kumanogoh A, Takeda K, Okada Y.
    • Journal Title

      Ann Rheum Dis

      Volume: 79(1) Pages: 103-111

    • DOI

      10.1136/annrheumdis-2019-215743

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles2019

    • Author(s)
      Matsumoto Yuki、Kinjo Takeshi、Motooka Daisuke、Nabeya Daijiro、Jung Nicolas、Uechi Kohei、Horii Toshihiro、Iida Tetsuya、Fujita Jiro、Nakamura Shota
    • Journal Title

      Emerging Microbes & Infections

      Volume: 8 Pages: 1043-1053

    • DOI

      10.1080/22221751.2019.1637702

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Complex Class 1 Integron in a Clinical Escherichia coli Strain From Vietnam Carrying Both mcr-1 and blaNDM?12019

    • Author(s)
      Le-Vo Hong-Ngoc、Tran Phuong Thi-Bich、Le Lien、Matsumoto Yuki、Motooka Daisuke、Nakamura Shota、Jones James W.、Iida Tetsuya、Cao Van
    • Journal Title

      Frontiers in Microbiology

      Volume: 10

    • DOI

      10.3389/fmicb.2019.02472

    • Related Report
      2019 Research-status Report
  • [Journal Article] Deep Learning Approach for Pathogen Detection Through Shotgun Metagenomics Sequence Classification2019

    • Author(s)
      Hsu Ying-Feng、Ito Makiko、Maruyama Takumi、Matsuoka Morito、Jung Nicolas、Matsumoto Yuki、Motooka Daisuke、Nakamura Shota
    • Journal Title

      Artificial Intelligence in Medicine

      Volume: - Pages: 24-30

    • DOI

      10.1007/978-3-030-21642-9_4

    • Related Report
      2019 Research-status Report
  • [Remarks] プレスリリース

    • URL

      http://www.biken.osaka-u.ac.jp/achievement/research/2019/130

    • Related Report
      2019 Research-status Report

URL: 

Published: 2019-04-18   Modified: 2023-01-30  

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