Skip to main content
SpringerLink
Log in

Development of DNA microarray for pathogen detection

  • Published:
Biotechnology and Bioprocess Engineering Aims and scope Submit manuscript

Abstract

Pathogens pose a significant threat to humans, animals, and plants. Consequently, a considerable effort has been devoted to developing rapid, convenient, and accurate assays for the detection of these unfavorable organisms. Recently, DNA-microarray based technology is receiving much attention as a powerful tool for pathogen detection. After the target gene is first selected for the unique identification of microorganisms, species-specific probes are designed through bioinformatic analysis of the sequences, which uses the information present in the databases. DNA samples, which were obtained from reference and/or clinical isolates, are properly processed and hybridized with species-specific probes that are immobilized on the surface of the microarray for fluorescent detection. In this study, we review the methods and strategies for the development of DNA microarray for pathogen detection, with the focus on probe design.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. David, A., A. Novis, C. D. Jane, B. S. Ron, G. R. Stephen, and K. W. Molly (2001) Solitary blood cultures.Arch. Pathol. Lab. Med. 125: 1290–1294.

    Google Scholar 

  2. Tillib, S. V. and A. D. Mirzabekov (2001) Advances in the analysis of DNA sequence variations using oligonucleotide microchip technology.Curr. Opin. Biotechnol. 12: 53–58.

    Article  CAS  Google Scholar 

  3. Lockhart, D. J., H. Dong, M. C. Byrne, M. T. Follettie, M. V. Gallo, M. S. Chee, M. Mittmann, C. Wang, M. Kobayashi, H. Horton, and E. L. Brown (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays.Nat. Biotechnol. 14: 1675–1680.

    Article  CAS  Google Scholar 

  4. Wilson, W. J., C. L. Strout, T. Z. Desantis, J. L. Stilwell, A. V. Carrano, and G. L. Andersen (2002) Sequence-specific identification of 18 pathogenic microorganisms using microarray technology.Mol Cell Probe 16: 119–127.

    Article  CAS  Google Scholar 

  5. Wang, R. F., M. L. Beggs, L. H. Robertson, and C. E. Cerniglia (2002) Design and evaluation of microarray oligonucleotidementhod for the detection of human intestinal bacteria in fecal samples.FEMS Microbiol. Lett. 213 (2): 175–182.

    Article  CAS  Google Scholar 

  6. Rudi, K., H. K. Nogva, B. Moen, H. Nissen, S. Bredholt, T. Moretro, K. Naterstad, and A. Holck, (2002) Development and application of new nucleic acid-based technologies for microbial community analyses in foods.Int. J. Food Microbiol. 78: 171–180.

    Article  CAS  Google Scholar 

  7. Fox, G. E., J. D. Wisotzkey, and P. Jurtshuk (1992) How close is close: 16S rRNA sequence identify may not be sufficient to guarantee species identity.Int. J. Syst. Bacteriol. 42: 166–170.

    Article  CAS  Google Scholar 

  8. Amann, R. and W. Ludwig (2000) Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology.FEMS Microbiol. Rev. 24: 555–565.

    Article  CAS  Google Scholar 

  9. Woose, C. R. (1987) Bacterial evolution.Microbiol. Rev. 51: 221–271.

    Google Scholar 

  10. Kisand, V., R. Cuadros, and J. Wikner (2002) Phylogeny of culturable estuarine bacteria catabolizing riverine organic matter in the Northern Baltic sea.Appl. Environ. Microbial. 68: 379–388.

    Article  CAS  Google Scholar 

  11. Koizumi, Y., J. J. Kelly, T. Nakagawa, H. Urakawa, S. El-Fantroussi, S. Al-Muzaini, M. Fukui, Y. Urushigawa, and D. A. Stahl (2002) Parallel characterization of anaerobic toluene- and ethylbenzene-degrading consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology.Appl. Environ. Microbiol. 68: 3215–3225.

    Article  CAS  Google Scholar 

  12. Maidak, B. L., J. R. Cole, C. T. Parker Jr, G. M. Garrity, R. Overbe, S. Pramanik, T. M. Schmidt, J. M. Tiedje, and C. R. Woese (1999) A new version of the RDP (Ribosomal Database Project).Nucleic Acids Res. 27: 171–173.

    Article  CAS  Google Scholar 

  13. Park, H., H. Jang, C. Kim, B. Chung, C. L. Chang, S. K. Park, and S. Song (2000) Detection and identification ofmycobacteria by amplification of the internal transcribed spacer regions with genus-and species-specific PCR primers.J. Clin. Microbiol. 38: 4080–4085.

    CAS  Google Scholar 

  14. Anthony, R. M., T. J. Brown, and G. L. French (2000) Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array.J. Clin. Microbiol. 38: 781–788.

    CAS  Google Scholar 

  15. Volokhov, D., V. Chizhikov, K. Chumakov, and A. Rasooly (2003) Microarray-based identification of thermophilicCampylobacter jejuni, C. coli. C. lari, andC. upsaliensis.J. Clin. Microbiol. 41: 4071–4080.

    Article  CAS  Google Scholar 

  16. Cho, J. C. and J. M. Tiedje (2001) Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays.Appl. Environ. Microbiol. 67: 3677–3682.

    Article  CAS  Google Scholar 

  17. Raskin, L., L. K. Poulsen, D. R. Noguera, B. E. Rittmann, and D. A. Stahl (1994) Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization.Appl. Environ. Microbiol. 60: 1241–1248.

    CAS  Google Scholar 

  18. Muyzer, G., E. C. De Waal, and A. G. Uitterlinden (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA.Appl. Environ. Microbiol. 59: 695–700.

    CAS  Google Scholar 

  19. Liu, W. T., T. L. Marsh, H. Cheng, and L. J. Forney (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA.Appl. Environ. Microbiol. 63: 4516–4522.

    CAS  Google Scholar 

  20. Yoo, S. Y., K. H. Chang, S. M. Yoo, S. Y. Park, N. C. Yoo, K. C. Keum, W. M. Yoo, J. M. Kim, and S. Y. Lee (2002) Design of ITS and 23S rDNA-targeted probes and its usefulness for the identification of bacterial pathogens.Genome Informatics 13: 589–590.

    CAS  Google Scholar 

  21. Van de Peer, Y., E. Robbrecht, S. de Hoog, A. Caers, P. de Rijk, and R. de Wachter (1999) Database on the structure of small subunit ribosomal RNA.Nucleic Acids Res. 27: 17–183.

    Article  Google Scholar 

  22. Li, F. and G. D. Stormo (2001) Selection of optimal DNA oligos for gene expression arrays.Bioinformatics 17: 107–1076.

    Article  Google Scholar 

  23. Rozen, S. and H. J. Skaletsky (2000) Primer 3 on the WWW for general users and for biologist programmers.Methods Mol. Biol. 132: 365–386.

    CAS  Google Scholar 

  24. Rouillard, J. M., C. J. Herbert, and M. Zuker (2002) OligoArray: Genome-scale oligonucleotide design for microarrays.Bioinformatics 18: 486–487.

    Article  CAS  Google Scholar 

  25. Varotto, C., E. Richly, F. Salamini, and D. Leister (2001) GST-PRIME: A genome-wide primer design software for the generation of gene sequence tags.Nucleic Acids Res. 29: 4373–4377.

    Article  CAS  Google Scholar 

  26. Bertilsson, S., C. M. Cavanaugh, and M. F. Polz (2002) Sequencing-independent method to generate oligonucleotide probes targeting a variable region in bacterial 16S rRNA by PCR with detachable primers.Appl. Environ. Microbiol. 68: 6077–6086.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Medigenes Co., 713 Suseo-dong, Gangnam-gu, 135-539, Seoul, Korea

    Seung Min Yoo & So Young Yoo

  2. Department of Chemical & Biomolecular Engineering and BioProcess Engineering Research Center, KAIST, 373-1 Guseong-dong, Yuseong-gu, 305-701, Daejeon, Korea

    So Young Yoo & Sang Yup Lee

  3. Department of Radiation Oncology, Yonsei University College of Medicine, 134 Sinchon-dong, Seodaemun-gu, 120-752, Seoul, Korea

    Ki Chang Keum

  4. Department of Internal Medicine, Yonsei University College of Medicine, 134 Sinchon-dong, Seodaemun-gu, 120-752, Seoul, Korea

    Jun Yong Choi, Kyung Hee Chang & June Myung Kim

  5. Department of Oncology and Cancer Center, Yonsei University College of Medicine, 134 Sinchon-dong, Seodaemun-gu, 120-752, Seoul, Korea

    Nae Choon Yoo

  6. Department of Plastic & Reconstructive Surgery, Yonsei University College of Medicine, 134 Sinchon-dong, Seodaemun-gu, 120-752, Seoul, Korea

    Won Min Yoo

  7. Harvard School of Dental Medicine, 188 Longwood Avenue, 02115, Boston, MA, USA

    Duke Lee

  8. Department of Medicine and Pharmacology, Yale University School of Medicine, Cedar Street, 06510, New Haven, CT, USA

    Ki Chang Keum & Won Min Yoo

  9. CambridgeMED Co., 44 Brattle street, 02138, Cambridge, MA, USA

    Duke Lee

Authors
  1. Seung Min Yoo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ki Chang Keum
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. So Young Yoo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jun Yong Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kyung Hee Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Nae Choon Yoo
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Won Min Yoo
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. June Myung Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Duke Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Sang Yup Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sang Yup Lee.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yoo, S.M., Keum, K.C., Yoo, S.Y. et al. Development of DNA microarray for pathogen detection. Biotechnol Bioproc E 9, 93–99 (2004). https://doi.org/10.1007/BF02932990

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF02932990

Keywords

Search

Navigation