Dynamics of clinically derived drug-resistant plasmid by plasmid network analysis

• Project/Area Number: 15K08488
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Bacteriology (including mycology)
• Research Institution: National Institute of Infectious Diseases
• Principal Investigator: Yamashita Akifumi 国立感染症研究所, 病原体ゲノム解析研究センター, 主任研究官 (00573180)
• Research Collaborator: KURODA MAKOTO 国立感染症研究所, 病原体ゲノム解析研究センター, センター長 (80317411)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000); Fiscal Year 2017: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2015: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: プラスミド / 薬剤耐性 / ネットワーク解析 / バイオインフォマティクス / 臨床由来株 / 不和合性タイピング / 薬剤耐性遺伝子 / webアプリ / 不和合性タイプ

Outline of Final Research Achievements

In this study, we created a web application named open iPAT to explore the relationship of plasmids in a bird's-eye view by using network analysis techniques by utilizing the fact that related plasmids share genes of the same origin. The open iPAT enabled not only to display related plasmids registered in the public database on the network diagram, but also to display the list of drug resistance genes, incompatibility typing, collected countries, hosts, collection year, etc. In addition, we implemented a function to graphically display the results by pangenomic analysis and core genome analysis, making it possible to analyze the relationship of plasmids in detail.

Research Products

• [Journal Article] Decrease in the prevalence of extended-spectrum cephalosporin-resistant Salmonella following cessation of ceftiofur use by the Japanese poultry industry (2018)
  • Author(s): Shigemura Hiroaki、Matsui Mari、Sekizuka Tsuyoshi、Onozuka Daisuke、Noda Tamie、Yamashita Akifumi、Kuroda Makoto、Suzuki Satowa、Kimura Hirokazu、Fujimoto Shuji、Oishi Kazunori、Sera Nobuyuki、Inoshima Yasuo、Murakami Koichi
  • Journal Title: International Journal of Food Microbiology Volume: 274 Pages: 45-51
  • DOI: 10.1016/j.ijfoodmicro.2018.03.011
  • Peer Reviewed
• [Journal Article] Isolation and Complete Genome Sequencing of Zika Virus Imported from the Dominican Republic to Japan (2018)
  • Author(s): Ozawa H, Tajima S, Nakayama E, Kato K, Yamashita A, Sekizuka T, Kuroda M, Usuku S.
  • Journal Title: Japanese Journal of Infectious Diseases Volume: 71 Issue: 1 Pages: 72-74
  • DOI: 10.7883/yoken.JJID.2017.256
  • NAID: 130006317353
  • ISSN: 1344-6304, 1884-2836
  • Peer Reviewed / Open Access
• [Journal Article] A summary of the imported cases of Chikungunya fever in Japan from 2006 to June 2016 (2017)
  • Author(s): Nakayama Eri、Tajima Shigeru、Kotaki Akira、Shibasaki Ken-ichi、Itokawa Kentaro、Kato Kengo、Yamashita Akifumi、Sekizuka Tsuyoshi、Kuroda Makoto、Tomita Takashi、Saijo Masayuki、Takasaki Tomohiko
  • Journal Title: Journal of Travel Medicine Volume: 25 Issue: 1
  • DOI: 10.1093/jtm/tax072
  • Peer Reviewed
• [Journal Article] Molecular Evolution of the VP1 Gene in Human Norovirus GII.4 Variants in 1974?2015 (2017)
  • Author(s): Motoya Takumi、Nagasawa Koo、Matsushima Yuki、Nagata Noriko、Ryo Akihide、Sekizuka Tsuyoshi、Yamashita Akifumi、Kuroda Makoto、Morita Yukio、Suzuki Yoshiyuki、Sasaki Nobuya、Katayama Kazuhiko、Kimura Hirokazu
  • Journal Title: Frontiers in Microbiology Volume: 8
  • DOI: 10.3389/fmicb.2017.02399
  • Peer Reviewed / Open Access
• [Journal Article] Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids (2017)
  • Author(s): Sekizuka Tsuyoshi、Kawanishi Michiko、Ohnishi Mamoru、Shima Ayaka、Kato Kengo、Yamashita Akifumi、Matsui Mari、Suzuki Satowa、Kuroda Makoto
  • Journal Title: Scientific Reports Volume: 7 Issue: 1
  • DOI: 10.1038/s41598-017-01082-y
  • Peer Reviewed / Open Access
• [Journal Article] Characterization of the Pathogenicity of Streptococcus intermedius TYG1620 Isolated from a Human Brain Abscess Based on the Complete Genome Sequence with Transcriptome Analysis and Transposon Mutagenesis in a Murine Subcutaneous Abscess Model. (2016)
  • Author(s): Hasegawa N, Sekizuka T, Sugi Y, Kawakami N, Ogasawara Y, Kato K, Yamashita A, Takeuchi F, Kuroda M
  • Journal Title: Infect Immun. Volume: 85 Issue: 2
  • DOI: 10.1128/iai.00886-16
  • Peer Reviewed / Open Access
• [Journal Article] Prevalence of Colistin Resistance Gene mcr-1 and Absence of mcr-2 in Escherichia coli Isolated from Healthy Food-Producing Animals in Japan. (2016)
  • Author(s): Kawanishi M, Abo H, Ozawa M, Uchiyama M, Shirakawa T, Suzuki S, Shima A, Yamashita A, Sekizuka T, Kato K, Kuroda M, Koike R, Kijima M.
  • Journal Title: Antimicrob Agents Chemother. Volume: 61 Issue: 1
  • DOI: 10.1128/aac.02057-16
  • Peer Reviewed / Open Access
• [Journal Article] Two different dengue virus strains in the Japanese epidemics of 2014. (2016)
  • Author(s): Nakayama E, Kotaki A, Tajima S, Kawada M, Miura K, Gemma A, Adachi T, Sekizuka T, Kato K, Yamashita A, Moi ML, Ikeda M, Yagasaki K, Shibasaki K, Saijo M, Kuroda M, Takasaki T.
  • Journal Title: Virus Genes. Volume: 52 Issue: 5 Pages: 722-6
  • DOI: 10.1007/s11262-016-1356-4
  • Peer Reviewed
• [Journal Article] DGV: Dengue Genographic Viewer. (2016)
  • Author(s): Yamashita A, Sakamoto T, Sekizuka T, Kato K, Takasaki T, Kuroda M.
  • Journal Title: Front Microbiol. Volume: 7 Pages: 875-875
  • DOI: 10.3389/fmicb.2016.00875
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Distribution and relationships of antimicrobial resistance determinants among extended-spectrum cephalosporin or carbapenem-resistant Escherichia coli isolated from rivers and sewage treatment plants in India. (2016)
  • Author(s): Masato Akiba, Tsuyoshi Sekizuka, Akifumi Yamashita, Makoto Kuroda, Yuki Fujii, Misato Murata, Ken-Ichi Lee, Derrick Ian Joshua, Keshava Balakrishna, Indira Bairy, Kaushik Subramanian, Padma Krishnan, Natesan Munuswamy, Ravindra K Sinha, Taketoshi Iwata, Masahiro Kusumoto, Keerthi S Guruge
  • Journal Title: Antimicrobial agents and chemotherapy Volume: 60 Issue: 5 Pages: 2972-2980
  • DOI: 10.1128/aac.01950-15
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] VirusTAP: Viral Genome-Targeted Assembly Pipeline (2016)
  • Author(s): Akifumi Yamashita, Tsuyoshi Sekizuka, Makoto Kuroda
  • Journal Title: Frontiers in Microbiology Volume: 7 Pages: 32-32
  • DOI: 10.3389/fmicb.2016.00032
  • Peer Reviewed / Open Access
• [Journal Article] Characterization of the gut microbiota of Kawasaki disease patients by metagenomic analysis (2015)
  • Author(s): Akiko Kinumaki, Tsuyoshi Sekizuka, Hiromichi Hamada, Kengo Kato, Akifumi Yamashita, Makoto Kuroda
  • Journal Title: Frontiers in Microbiology Volume: 6 Pages: 824-824
  • DOI: 10.3389/fmicb.2015.00824
  • Peer Reviewed / Open Access
• [Journal Article] TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis Using Short-Read Whole-Genome Sequencing. (2015)
  • Author(s): Tsuyoshi Sekizuka, Akifumi Yamashita, Yoshiro Murase, Tomotada Iwamoto, Satoshi Mitarai, Seiya Kato, Makoto Kuroda
  • Journal Title: PloS one Volume: 10 Issue: 11 Pages: 142951-142951
  • DOI: 10.1371/journal.pone.0142951
  • Peer Reviewed / Open Access
• [Presentation] Prediction Tool for Drug-resistant Genetic Marker Based on Whole Genome Sequence of TB (2017)
  • Author(s): 山下明史、加藤健吾、岩本朋忠、関塚剛史、村瀬良朗、瀧井猛将、手洗聡、加藤誠也、黒田誠
  • Organizer: 第90回日本細菌学会総会
  • Place of Presentation: 宮城県仙台市青葉区青葉山 仙台国際センター
  • Year and Date: 2017-03-19
• [Presentation] Genetic prediction tool for antimicrobial susceptibility of Mycobacterium tuberculosis using TGS-TBamr. (2017)
  • Author(s): Akifumi Yamashita, Tomotada Iwamoto, Tsuyoshi Sekizuka, Yoshiro Murase, Takemasa Takii, Satoshi Mitarai, Kengo Kato, Seiya Kato, and Makoto Kuroda
  • Organizer: ICC2017
  • Int'l Joint Research
• [Presentation] DGV: Dengue Genographic Viewer (2017)
  • Author(s): Akifumi Yamashita, Tsuyoshi Sekizuka, Kengo Kato, Tomohiko Takasaki, Makoto Kuroda
  • Organizer: 第52回日本脳炎ウイルス生態学研究会
• [Presentation] Total Genotyping Solution for Mycobacterium tuberculosis (TGS-TB) による結核菌薬剤耐性マーカー検出と感受性予測法の構築 (2017)
  • Author(s): 山下明史、瀧井猛将、御手洗聡、黒田誠
  • Organizer: 第65回化学療法学会学術集会
• [Presentation] DGV: Gengue Genographic Viewer (2016)
  • Author(s): 山下明史、関塚剛史、加藤健吾、高崎智彦、黒田誠
  • Organizer: JOINT INTERNATIONAL TROPICAL MEDICINE MEETING 2016
  • Place of Presentation: Amari Watergate, Bangkok, Thailand
  • Year and Date: 2016-12-07
  • Int'l Joint Research
• [Presentation] Virus genome-targeted assembly pipeline: VirusTAP (2016)
  • Author(s): 山下明史、関塚剛史、黒田誠
  • Organizer: 第5回生命医薬情報学連合大会
  • Place of Presentation: 東京都江東区青海 東京国際交流プラザ平成
  • Year and Date: 2016-09-29
• [Presentation] DGV: Gengue Genographic Viewer (2016)
  • Author(s): 山下明史、関塚剛史、加藤健吾、高崎智彦、黒田誠
  • Organizer: The 11th Japan-China International Conference of Virology
  • Place of Presentation: 香川県観音寺市琴弾荘
  • Year and Date: 2016-07-01
  • Int'l Joint Research
• [Presentation] プラスミドネットワーク解析ツールiPAT (inter Plasmid Analyzing Tool) (2016)
  • Author(s): 山下明史、黒田誠
  • Organizer: 第64回日本化学療法学会総会
  • Place of Presentation: 神戸市中央区港島中町 神戸国際会議場
  • Year and Date: 2016-06-09
• [Presentation] TGS-TB: Total Genotyping Solution for M. tuberculosis using short-read whole-genome sequencing (2016)
  • Author(s): Tsuyoshi Sekizuka, Akifumi Yamashita, Yoshihiro Murase, Tomotada Iwamoto, Satoshi Mitarai, Seiya Kato, Makoto Kuroda
  • Organizer: 第89回日本細菌学会
  • Place of Presentation: 大阪国際交流センター
  • Year and Date: 2016-03-23
• [Presentation] Geographical view of dengue genotype distribution (2015)
  • Author(s): Akifumi Yamashita, Tetsuya Sakamoto, Tsuyoshi Sekizuka, and Makoto Kuroda
  • Organizer: DENGUE SURVEILLANCE: INFORMATION-SHARING AMONG ASIAN COUNTRIES FOR A BETTER PREPARED REGION
  • Place of Presentation: 国立感染症研究所戸山庁舎
  • Year and Date: 2015-09-30
  • Int'l Joint Research
• [Presentation] TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis using short-read whole-genome sequencing (2015)
  • Author(s): Tsuyoshi Sekizuka, Akifumi Yamashita, Yoshihiro Murase, Tomotada Iwamoto, Satoshi Mitarai, Seiya Kato, Makoto Kuroda
  • Organizer: 1st ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens
  • Place of Presentation: Omni Shoreham Hotel 2500 Calvert St NW, Washington, DC
  • Year and Date: 2015-09-24
  • Int'l Joint Research
• [Presentation] TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis using short-read whole-genome sequencing (2015)
  • Author(s): Tsuyoshi Sekizuka, Akifumi Yamashita, Yoshiro Murase, Tomotada Iwamoto, Satoshi Mitarai, Seiya Kato, Makoto Kuroda
  • Organizer: 8th Meeting on Global Microbial Identifier (GMI)
  • Place of Presentation: Sunworld Dynasty Hotel, 50 Wangfujing Avenue, Beijing, China
  • Year and Date: 2015-05-11
  • Int'l Joint Research
• [Remarks] inter Plasmid Analyzing Tool (open iPAT)
  • URL: https://gph.niid.go.jp/cgi-bin/ipat/index.cgi
• [Remarks] TGS-TB
  • URL: https://gph.niid.go.jp/tgs-tb/
• [Remarks] VirusTAP
  • URL: https://gph.niid.go.jp/cgi-bin/virustap/index.cgi
• [Remarks] GV: Dengue Genographic Viewer
  • URL: https://gph.niid.go.jp/genepid-j/dgv
• [Remarks] DGV: Dengue Genographic Viewer
  • URL: https://gph.niid.go.jp/geograph/dengue/content/genomemap
• [Remarks] TGS-TB
  • URL: https://gph.niid.go.jp/tgs-tb/index_tb.html