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Development of new classification system for pathogenic Nocardia based on whole genome sequences and microarray analysis

Research Project

Project/Area Number 17590385
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Bacteriology (including Mycology)
Research InstitutionChiba University

Principal Investigator

MIKAMI Yuzuru  Chiba University, Research Center for Pathogenic Fungi and Microbial Toxicoses, Professor, 真菌医学研究センター, 教授 (40092100)

Co-Investigator(Kenkyū-buntansha) GONOI Tohru  Chiba University, Research Center for Pathogenic Fungi and Microbial Toxicoses, Assistant Professor, 真菌医学研究センター, 講師 (30134365)
Project Period (FY) 2005 – 2006
Project Status Completed (Fiscal Year 2006)
Budget Amount *help
¥3,400,000 (Direct Cost: ¥3,400,000)
Fiscal Year 2006: ¥1,600,000 (Direct Cost: ¥1,600,000)
Fiscal Year 2005: ¥1,800,000 (Direct Cost: ¥1,800,000)
KeywordsNocardia / new classification system / gryB gene / genome / 16S rDNA / siderophore / 種の鑑別法
Research Abstract

We reported the genomic sequence of Nocardia farcinica IFM 10152 in 2004. Based on the sequence, we found and analyzed genes which were specific to this species. DNA of size 238 bp specific to N. farcinica was selected for further studies. A section of this DNA partially encoded a hypothetical protein (nfa 29510), and the remaining was a non-coding region located next to a membrane protein (nfa 29520) gene. From these genetic analyses, a specific PCR primer for N. farcinica strains was designed, and their specificity was confirmed. In addition, the primer was found to be useful for the detection of N. farcinica in the blood of mice with experimental nocardiosis. The primer was also found to be useful for RealTime PCR.
Based on the sequence of gyrB gene from N. farcinica IFM 10152, a modified PCr primer for the efficient amplification of the gene in Nocardia was designed. The gyrB gene sequences of all 60 Nocardia type species were analyzed, and a phylogenetic tree was constructed. This allowed the Nocardia species to be clearly differentiated from Mycobacterium and Rhodococcus, with homogeneity values of 82% and 76%, respectively.
In bacterial classification, sequence of 16S rDNA is most commonly used, with no exception in Nocardia. As for the width of difference among the 60 Nocardia species, their values are distributed from 94.5 to 100.0%. However, in gyrB which we analyzed, this difference markedly increased to 82.4 to 99.9%. Usefulness of gyrB sequence for the classification of these species was confirmed, and we proposed it as a new classification system n Nocardia. Although 1,200 bp sequence of gyrB was used in the present study, further work is in progress for the development of a system using less than 600 bp from variation domains in the gene.

Report

(3 results)
  • 2006 Annual Research Report   Final Research Report Summary
  • 2005 Annual Research Report
  • Research Products

    (22 results)

All 2007 2006 2005

All Journal Article (21 results) Book (1 results)

  • [Journal Article] Construction of a pair of practical Nocardia-Escherichia coli shuttle vectors.2007

    • Author(s)
      Chiba K
    • Journal Title

      Jpn J Infect Dis 60

      Pages: 45-47

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Nocardia terpenica sp. nov., isolated from Japanese patients with nocardiosis.2007

    • Author(s)
      Hoshino Y
    • Journal Title

      Int J Syst Evol Microbiol (In press)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Nocardia terpenica sp. nov., isolated from Japanese patients with nocardiosis.2007

    • Author(s)
      Hoshino Y
    • Journal Title

      Int J Syst Evol Microbiol (in press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Construction of a pair of practical Nocardia-Escherichia coli shuttle vectors.2007

    • Author(s)
      Chiba K, et al.
    • Journal Title

      Jpn J Infect Dis 60

      Pages: 45-47

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Nocardia terpenica sp. nov., isolated from Japanese patients with nocardiosis.2007

    • Author(s)
      Hoshino Y, et al.
    • Journal Title

      Int J Syst Evol Microbiol In press

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Nocardia exalbida sp. nov., isolated from Japanese patients with nocardiosis.2006

    • Author(s)
      Iida S
    • Journal Title

      Int J Syst Evol Microbiol 56

      Pages: 1193-1196

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] First clinical isolate of Nocardia carnea, Nocardia elegans, Nocardia paucivorans, Nocardia puris and Nocardia takedensis from patients in Japan.2006

    • Author(s)
      Watanabe K
    • Journal Title

      Jap J Med Mycol 47

      Pages: 85-89

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Gordonia araii sp. nov. and Gordonia effusa sp. nov. isolated from patients in Japan.2006

    • Author(s)
      Kageyama A
    • Journal Title

      Int J Syst Evol Microbiol 56

      Pages: 1817-1821

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Majority of Actinomadura clinical isolates from sputa or bronchoalveolar lavage fluid in Japan belongs to the cluster of Actinomadura cremea and Actinomadura nitritigenes, and the description of Actinomadura chibensis sp. nov.2006

    • Author(s)
      Hanafy A
    • Journal Title

      Mycopathologia 164

      Pages: 281-287

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Nocardia exalbida sp.nov., isolated from Japanese patients with nocardiosis.2006

    • Author(s)
      Iida S
    • Journal Title

      Int J Syst Evol Microbiol 56

      Pages: 1193-1196

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Majority of Actinomadura clinical isolates from sputa or bronchoalveolar lavage fluid in Japan belongs to the cluster of Actinomadura cremea and Antinomadura nitritigenes, and the description of Actinomadura chibensis sp. nov.2006

    • Author(s)
      Hanafy A
    • Journal Title

      Mucopathologia 164

      Pages: 281-287

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Nocardia exalbida sp. nov.,isolated from Japanese patients with nocardiosis.2006

    • Author(s)
      Iida S, et al.
    • Journal Title

      Int J Syst Evol Microbiol 56

      Pages: 1193-1196

    • Related Report
      2006 Annual Research Report
  • [Journal Article] First clinical isolate of Nocardia carnea, Nocardia elegans, Nocardia paucivorans, Nocardia puris and Nocardia takedensis from patients in Japan.2006

    • Author(s)
      Waranabe K, et al.
    • Journal Title

      Jap J Med Mycol 47

      Pages: 85-89

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Gordonia araii sp. nov. and Gordonia effusa sp. nov. isolated from patients in Japan.2006

    • Author(s)
      Kageyama A, et al.
    • Journal Title

      Int J Syst Evol Microbiol 56

      Pages: 1817-1821

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Majority of Actinomadura clinical isolates from sputa or bronchoalveolar lavage fluid in Japan belongs to the cluster of Actinomadura cremea and Actinomadura nitritigenes, and the description of Actinomadura chibensis sp. nov.2006

    • Author(s)
      Hanafy A, et al.
    • Journal Title

      Mycopathologia 164

      Pages: 281-287

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Nocardia anaemiae sp. nov. isolated from an immunocompromised patient and first isolation report of Nocardia vinacea from human2005

    • Author(s)
      Kageyama A, et al.
    • Journal Title

      Japanese Journal of Medical Mycology 46

      Pages: 21-26

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Gorodnia otitidis sp. nov., isolated from a patient with external otitis2005

    • Author(s)
      Iida S, et al.
    • Journal Title

      International Journal of Systematic and Evolutionary Microbiology 55

      Pages: 1871-1876

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Nocardia cyriacigeorgica is a significant pathogen of nocardiosis in Japan and Thailand2005

    • Author(s)
      Kageyama A, et al.
    • Journal Title

      Mycopathologia 160

      Pages: 15-19

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Nocardia concava sp. nov. isolated from Japanese patients2005

    • Author(s)
      Kageyama A, et al.
    • Journal Title

      International Journal of Systematic and Evolutionary Microbiology 55

      Pages: 2081-2083

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Biotransformation of bile acids by pathogenic Nocardia otitidiscaviarum and Amycolatopsis sp. strains2005

    • Author(s)
      Mukai A, et al.
    • Journal Title

      Journal of Antibiotics 58

      Pages: 356-360

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Characterization of clinical isolates of pathogenic Nocardia strains and related actinomycetes in Thailand2005

    • Author(s)
      Poonwan N, et al.
    • Journal Title

      Mycopathologia 159

      Pages: 361-368

    • Related Report
      2005 Annual Research Report
  • [Book] 感染症予防必携(第2版):放線菌症、ノカルジア症2005

    • Author(s)
      三上 襄(分担)
    • Total Pages
      675
    • Publisher
      (財)日本公衆衛生協会(山崎修道他編)
    • Related Report
      2005 Annual Research Report

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Published: 2005-04-01   Modified: 2016-04-21  

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