Development of infection diagnosis using 3rd generation sequencing

• Project/Area Number: 24890103
• Research Category: Grant-in-Aid for Research Activity Start-up
• Allocation Type: Single-year Grants
• Research Field: General medical chemistry
• Research Institution: Osaka University
• Principal Investigator: MOTOOKA Daisuke 大阪大学, 微生物病研究所, 特任研究員(常勤) (10636830)
• Project Period (FY): 2012-08-31 – 2014-03-31
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000); Fiscal Year 2013: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2012: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
• Keywords: メタゲノム / 次世代シークエンサー / 感染症 / メタゲノム解析 / 感染症診断 / バイオインフォマティクス

Research Abstract

Metagenomic analysis using 2nd generation sequencers is now widely used for comprehensive detection of pathogens in infectious diseases. This method with a single common protocol in clinical specimens doesn't depend on the type of microorganisms, overcoming the limitations of traditional methods. However, because this method detects only a part of genome information of pathogen, we can't get enough information to prevent infection disease. Here, I developed the method of infection diagnosis using 3rd generation sequencing. Third generation sequencing easily achieves higher degree of accuracy, less biased depth of coverage and a smaller number of contigs than other sequencing. The highly accurate complete genome analysis would develop the future genome epidemiology of pathogens.

Research Products

• [Journal Article] Complete Genome Sequence of Ureaplasma parvum Serovar 3 Strain SV3F4, Isolated in Japan (2014)
  • Author(s): Wu HN, Nakura Y, Motooka D, Nakamura S, Nishiumi F, Ishino S, Kawai Y, Tanaka T, Takeuchi M, Nakayama M, Fujita T, Yanagihara I
  • Journal Title: Genome Announc Volume: 2(3) Issue: 3
  • DOI: 10.1128/genomea.00256-14
  • Peer Reviewed / Open Access
• [Journal Article] Comprehensive metagenomic approach for detecting causative microorganisms in culture-negative infective endocarditis. (2014)
  • Author(s): Imai A, Gotoh K, Asano Y* (corresponding author), Yamada N, Motooka D, Fukushima M, Kanzaki M, Ohtani T, Sakata Y, Nishi H, Toda K, Sawa Y, Komuro I, Horii T, Iida T, Nakamura S, Takashima S.
  • Journal Title: Int J Cardiol. Volume: 172 Issue: 2 Pages: 288-9
  • DOI: 10.1016/j.ijcard.2013.12.197
  • Peer Reviewed
• [Journal Article] Severe respiratory failure due to co-infection with human metapneumovirus and Streptococcus pneumoniae. (2014)
  • Author(s): Seki M, Yoshida H, Gotoh K, Hamada N,Motooka D, Nakamura S, Yamamoto N, Hamaguchi S, Akeda Y, Watanabe H, Iida T, and Tomono K.
  • Journal Title: Respiratory Medicine Case Reports Volume: 12 Pages: 13-15
  • DOI: 10.1016/j.rmcr.2013.12.007
  • Peer Reviewed / Open Access
• [Journal Article] (2014)
  • Author(s): Seki M., Ohno H., Gotoh K., Motooka D., Nakamura S., Iida T., Miyazaki Y., Tomono K.
  • Journal Title: IDCases Volume: 1 Issue: 1 Pages: 5-8
  • DOI: 10.1016/j.idcr.2014.01.001
  • Peer Reviewed / Open Access
• [Journal Article] Severe respiratory failure due to co-infection with human metapneumovirus and Streptococcus pneumoniae (2014)
  • Author(s): Seki M, Yoshida H, Gotoh K, Hamada N, Motooka D, Nakamura S, Yamamoto N, Hamaguchi S, Akeda Y, Watanabe H, Iida T, Tomono K
  • Journal Title: Respiratory Medicine Case Reports Volume: 12 Pages: 13-15
  • Peer Reviewed
• [Presentation] A Database for Rapid Detection of Pathogens in Infectious Diseases (2014)
  • Author(s): Daisuke Motooka
  • Organizer: Asian-African Research Forum on Emerging and Reemerging Infection 2014
  • Place of Presentation: 仙台国際センター
• [Presentation] A Database for Rapid Detection of Pathogens in Infectious Diseases (2014)
  • Author(s): Daisuke Motooka, Kazuyoshi Gotoh, Shota Nakamura, Toshihiro Horii
  • Organizer: Asian-African Research Forum on Emerging and Reemerging Infections - 2014
  • Place of Presentation: 仙台国際センター
• [Presentation] メタゲノミック診断用データベース(iMetDB)の構築 (2014)
  • Author(s): 元岡大祐、後藤和義、後藤直久、中村昇太、飯田哲也、安永照雄、堀井俊宏
  • Organizer: 第8回 日本ゲノム微生物学会年会
  • Place of Presentation: 東京農業大学
• [Presentation] メタゲノミック診断法の高速解析パイプラインの構築 (2013)
  • Author(s): 元岡大祐
  • Organizer: NGS現場の会第三回研究会
  • Place of Presentation: 神戸国際会議場
• [Presentation] 第2・第3世代シークエンスデータを使ったCLC Genomics WorkbenchによるDe Novoアセンブリ (2013)
  • Author(s): 宮本真理、元岡大祐
  • Organizer: NGS現場の会第三回研究会
  • Place of Presentation: 神戸国際会議場
• [Presentation] 感染性心内膜炎におけるメタゲノム解析 (2013)
  • Author(s): 朝野仁裕、元岡大祐
  • Organizer: NGS現場の会第三回研究会
  • Place of Presentation: 神戸国際会議場
• [Presentation] 原因不明食中毒のメタゲノミック診断 (2013)
  • Author(s): 後藤和義、元岡大祐
  • Organizer: NGS現場の会第三回研究会
  • Place of Presentation: 神戸国際会議場
• [Presentation] 第２・第３世代シークエンスデータを使ったCLC Genomics WorkbenchによるDe novoアセンブリ (2013)
  • Author(s): 宮本真理、元岡大祐、後藤和義、後藤直久、中村昇太
  • Organizer: NGS現場の会第三回研究会
  • Place of Presentation: 神戸国際会議場
• [Remarks]
  • URL: http://imet.gen-info.osaka-u.ac.jp/
• [Remarks] 感染症メタゲノム研究分野
  • URL: http://imet.gen-info.osaka-u.ac.jp/