Detection of Pathogens in unknown fever cases using Nanopore Sequencer

• Project/Area Number: 15K14417
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Genome biology
• Research Institution: The University of Tokyo
• Principal Investigator: Suzuki Yutaka 東京大学, 大学院新領域創成科学研究科, 教授 (40323646)
• Co-Investigator(Kenkyū-buntansha): 山岸 潤也 北海道大学, 人獣共通感染症リサーチセンター, 准教授 (80535328)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2017: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2015: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
• Keywords: ゲノム / 簡易型シークエンサー / 熱帯感染症 / 迅速診断

Outline of Final Research Achievements

In this study, we have attempted to develop a method to detect pathogens in patients having unknown fevers. Even though we were not able to develop the method based on the random-primer amplification due to the high-level noises, we successfully develop the method, by which representative viral, bacterial and parasite pathogens, such as dengue viruses, 16S rRNA sequencing for pan-bacterial detections, and malaria parasites, respectively, could be robustly detected. We actually applied the developed method to diagnose the feverish patients in Manado, Indonesia. We have reported the successful diagnosis from more than 50 cases regarding their infecting pathogens. Moreover, it was possible to identify the SNPs in their genomes. Especially, we found that the SNPs residing in the drug-resistance related genes should have particularly important clinical relevance, when the therapeutic strategy of the patients should be decided.

Research Products

• [Int'l Joint Research] サムラトランギ大学(インドネシア)
• [Int'l Joint Research] サムラトランギ大学(インドネシア)
• [Journal Article] Serotyping dengue virus with isothermal amplification and a portable sequencer (2017)
  • Author(s): Yamagishi Junya、Runtuwene Lucky R.、Hayashida Kyoko、Mongan Arthur E.、Thi Lan Anh Nguyen、Thuy Linh Nguyen、Nhat Cam Nguyen、Limkittikul Kriengsak、Sirivichayakul Chukiat、Sathirapongsasuti Nuankanya、Frith Martin、Makalowski Wojciech、Eshita Yuki、Sugano Sumio、Suzuki Yutaka
  • Journal Title: Scientific Reports Volume: 7 Issue: 1 Pages: 3510-3510
  • DOI: 10.1038/s41598-017-03734-5
  • NAID: 120006337766
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] On Site Sequencing for Genotyping Pathogens of Tropical Diseases (2017)
  • Author(s): Yutaka Suzuki
  • Organizer: One Health International Seminar in Zoonoses and Wildlife
  • Int'l Joint Research / Invited
• [Presentation] Nanopore sequencing for genotyping pathogens of tropical diseases (2016)
  • Author(s): 鈴木穣
  • Organizer: Joint International Tropical Medicine Meeting 2016
  • Place of Presentation: バンコク、タイ
  • Year and Date: 2016-12-07
  • Int'l Joint Research / Invited
• [Presentation] MinION sequencing of malaria parasites (2016)
  • Author(s): 鈴木穣
  • Organizer: London Calling 2016
  • Place of Presentation: ロンドン、イギリス
  • Year and Date: 2016-05-26
  • Int'l Joint Research
• [Book] ナノポアシークエンサーMinION（RNA-Seq実験ハンドブック） (2016)
  • Author(s): 鈴木絢子、Lucky Runtuwene、阿部佳澄、鈴木穣
  • Total Pages: 280
  • Publisher: 羊土社