Development of a database for rapid detection of pathogens in infectious diseases

• Project/Area Number: 26870328
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Laboratory medicine; Infectious disease medicine
• 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): 2014-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2015: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2014: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: 感染症

Outline of Final Research Achievements

Metagenomic analysis using high-throughput sequencers is now widely applied for comprehensive detection of pathogens in infectious diseases. The pathogen identification approach is based on a similarity search with known proteins or nucleotides along with a taxonomic assignment of massive sequence reads produced by high-throughput sequencers. To adapt this method for clinical application, high-speed and low-cost calculation are essential. We constructed an infection Metagenomics DataBase (iMetDB), a database optimized for metagenomic diagnosis of infectious diseases. Data records of potential human pathogens, including bacteria, viruses, fungi and parasites, were collected from the GenBank database. To test the performance of databases, we carried out metagenomic analysis of influenza virus and norovirus infection cases. The resulting database enabled us perform up to a seven times faster calculation for the same pathogen detection efficiency.

Research Products

• [Journal Article] Next-generation sequencing (NGS) in the identification of encephalitis-causing viruses: Unexpected detection of human herpesvirus 1 while searching for RNA pathogens. (2015)
  • Author(s): Perlejewski K, Popiel M, Laskus T, Nakamura S, Motooka D, Stokowy T, Lipowski D, Pollak A, Lechowicz U, Caraballo CK, Stepien A, Radkowski M, Bukowska-Oska I.
  • Journal Title: J. Virol. Methods Volume: 226 Pages: 1-6
  • DOI: 10.1016/j.jviromet.2015.09.010
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Metagenomic analysis reveals dynamic changes of whole gut microbiota in the acute phase of intensive care unit patients (2015)
  • Author(s): Masahiro Ojima, Daisuke Motooka, Kentaro Shimizu, Kazuyoshi Gotoh, Ayumi Shintani, Kazuhisa Yoshiya, Shota Nakamura, Hiroshi Ogura, Tetsuya Iida, Takeshi Shimazu
  • Journal Title: Digestive Diseases and Sciences Volume: online Issue: 6 Pages: 1-7
  • DOI: 10.1007/s10620-015-4011-3
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Viral detection by high-throughput sequencing (2015)
  • Author(s): 4.Motooka D, Nakamura S, Hagiwara K, Nakaya T
  • Journal Title: Methods Mol Biol Volume: 1236 Pages: 125-34
  • DOI: 10.1007/978-1-4939-1743-3_11
  • ISBN: 9781493917426, 9781493917433
• [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] Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes. (2014)
  • Author(s): Miyamoto M, Motooka D, Gotoh K, Imai T, Yoshitake K, Goto N, Iida T, Yasunaga T, Horii T, Arakawa K, Kasahara M, Nakamura S.
  • Journal Title: BMC Genomics Volume: 15 Issue: 1 Pages: 699-699
  • DOI: 10.1186/1471-2164-15-699
  • Peer Reviewed / Open Access
• [Presentation] メタゲノミック診断用データベース(iMetDB)の構築と高速解析パイプライン (2015)
  • Author(s): 元岡大祐、後藤直久、飯田哲也、堀井俊宏、安永照雄、中村 昇太
  • Organizer: NGS現場の会第四回研究会
  • Place of Presentation: つくば国際会議場
  • Year and Date: 2015-07-01
• [Remarks] 感染症メタゲノム研究分野
  • URL: http://imet.gen-info.osaka-u.ac.jp/
• [Remarks] iMetDB
  • URL: http://imet.gen-info.osaka-u.ac.jp/en/imetdb.html