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Journal of Zhejiang University SCIENCE B

, Volume 9, Issue 4, pp 291–298 | Cite as

Using oligonucleotide suspension arrays for laboratory identification of bacteria responsible for bacteremia

  • Xiao-li Hou
  • Han-liang Jiang
  • Qing-yi Cao
  • Li-ying Zhao
  • Barbara J. Chang
  • Zhi Chen
Article

Abstract

The aim of this study was to develop and validate an oligonucleotide suspension array for rapid identification of 15 bacterial species responsible for bacteremia, particularly prevalent in Chinese hospitals. The multiplexed array, based on the QIAGEN LiquiChip Workstation, included 15 oligonucleotide probes which were covalently bound to different bead sets. PCR amplicons of a variable region of the bacterial 23S rRNA genes were hybridized to the bead-bound probes. Thirty-eight strains belonging to 15 species were correctly identified on the basis of their corresponding species-specific hybridization profiles. The results show that the suspension array, in a single assay, can differentiate isolates over a wide range of strains and species, and suggest the potential utility of suspension array system to clinical laboratory diagnosis.

Key words

Oligonucleotide array Bacteremia 23S rRNA Multiplexed detection 

CLC number

R37 

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References

  1. Anthony, R.M., Brown, T.J., French, G.L., 2000. Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array. J. Clin. Microbiol., 38(2):781–788.PubMedGoogle Scholar
  2. Armstrong, B., Stewart, M., Mazumder, A., 2000. Suspension arrays for high throughput, multiplexed single nucleotide polymorphism genotyping. Cytometry, 40(2):102–108. [doi:10.1002/(SICI)1097-0320(20000601)40:2<102::AID-C YTO3>3.3.CO;2-W]PubMedCrossRefGoogle Scholar
  3. Bovers, M., Diaz, M.R., Hagen, F., Spanjaard, L., Duim, B., Visser, C.E., Hoogveld, H.L., Scharringa, J., Hoepelman, I.M., Fell, J.W., Boekhout, T., 2007. Identification of genotypically diverse Cryptococcus neoformans and Cryptococcus gattii isolates by Luminex xMAP technology. J. Clin. Microbiol., 45(6):1874–1883. [doi:10.1128/JCM.00223-07]PubMedCrossRefGoogle Scholar
  4. Bryant, P.A., Venter, D., Robins-Browne, R., Curtis, N., 2004. Chips with everything: DNA microarrays in infectious diseases. Lancet Infect. Dis., 4(2):100–111. [doi:10.1016/S1473-3099(04)00930-2]PubMedCrossRefGoogle Scholar
  5. Cai, H., White, P.S., Torney, D., Deshpande, A., Wang, Z., Keller, R.A., Marrone, B., Nolan, J.P., 2000. Flow cytometry-based minisequencing: a new platform for high-throughput single-nucleotide polymorphism scoring. Genomics, 66(2):135–143. [doi:10.1006/geno.2000.6218]PubMedCrossRefGoogle Scholar
  6. Christensen, H., Nordentoft, S., Olsen, J., 1998. Phylogenetic relationships of Salmonella based on rRNA sequences. Int. J. Syst. Bacteriol., 48(Pt 2):605–610.PubMedCrossRefGoogle Scholar
  7. Corless, C.E., Guiver, M., Borrow, R., Edwards-Jones, V., Kaczmarski, E.B., Fox, A.J., 2000. Contamination and sensitivity issues with a real-time universal 16S rRNA PCR. J. Clin. Microbiol., 38(5):1747–1752.PubMedGoogle Scholar
  8. Dauga, C., 2002. Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies. Int. J. Syst. Evol. Microbiol., 52(Pt 2):531–547.PubMedGoogle Scholar
  9. Ding, L.P., Sun, Y.H., Wang, Q., Nian, H., 2004. Drug resistance of common bacteria isolated from blood and bone marrow. J. Chin. Med. Univ., 33(1):83–85 (in Chinese).Google Scholar
  10. Dunbar, S., Godbout, R., Newkirk, H., Hetzel, J., 2003a. Microsphere suspension array technology for SNP detection in cattle. IEEE Eng. Med. Biol. Mag., 22(4):158–162. [doi:10.1109/MEMB.2003.1237526]PubMedCrossRefGoogle Scholar
  11. Dunbar, S.A., Vander Zee, C.A., Oliver, K.G., Karem, K.L., Jacobson, J.W., 2003b. Quantitative, multiplexed detection of bacterial pathogens: DNA and protein applications of the Luminex LabMAP system. J. Microbiol. Methods, 53(2):245–252. [doi:10.1016/S0167-7012(03)00028-9]PubMedCrossRefGoogle Scholar
  12. Fukushima, M., Kakinuma, K., Hayashi, H., Nagai, H., Ito, K., Kawaguchi, R., 2003. Detection and identification of Mycobacterium species isolates by DNA microarray. J. Clin. Microbiol., 41(6):2605–2615. [doi:10.1128/JCM.41.6.2605-2615.2003]PubMedCrossRefGoogle Scholar
  13. Henry, M.R., Wilkins Stevens, P., Sun, J., Kelso, D.M., 1999. Real-time measurements of DNA hybridization on microparticles with fluorescence resonance energy transfer. Anal. Biochem., 276(2):204–214. [doi:10.1006/abio.1999.4344]PubMedCrossRefGoogle Scholar
  14. Kettman, J.R., Davies, T., Chandler, D., Oliver, K.G., Fulton, R.J., 1998. Classification and properties of 64 multiplexed microsphere sets. Cytometry, 33(2):234–243. [doi:10.1002/(SICI)1097-0320(19981001)33:2<234::AID-C YTO19>3.0.CO;2-V]PubMedCrossRefGoogle Scholar
  15. Khayr, W.F., CarMichael, M.J., Dubanowich, C.S., Latif, R.H., 2003. Epidemiology of bacteremia in the geriatric population. Am. J. Ther., 10(2):127–131. [doi:10.1097/00045391-200303000-00008]PubMedCrossRefGoogle Scholar
  16. Kwok, S., Higuchi, R., 1989. Avoiding false positives with PCR. Nature, 339(6221):237–238. [doi:10.1038/339237a0]PubMedCrossRefGoogle Scholar
  17. Leffers, H., Kjems, J., Ostergaard, L., Larsen, N., Garrett, R.A., 1987. Evolutionary relationships amongst archaebacteria. A comparative study of 23S ribosomal RNAs of a sulphur-dependent extreme thermophile, an extreme halophile and a thermophilic methanogen. J. Mol. Biol., 195(1):43–61. [doi:10.1016/0022-2836(87)90326-3]PubMedCrossRefGoogle Scholar
  18. Maiwald, M., Ditton, H.J., Sonntag, H.G., von Knebel Doeberitz, M., 1994. Characterization of contaminating DNA in Taq polymerase which occurs during amplification with a primer set for Legionella 5S ribosomal RNA. Mol. Cell. Probes, 8(1):11–14. [doi:10.1006/mcpr.1994.1002]PubMedCrossRefGoogle Scholar
  19. Nolan, J.P., Mandy, F.F., 2001. Suspension array technology: new tools for gene and protein analysis. Cell. Mol. Biol. (Noisy-le-grand), 47(7):1241–1256.Google Scholar
  20. Nolan, J.P., Sklar, L.A., 2002. Suspension array technology: evolution of the flat-array paradigm. Trends Biotechnol., 20(1):9–12. [doi:10.1016/S0167-7799(01)01844-3]PubMedCrossRefGoogle Scholar
  21. Peters, R.P., van Agtmael, M.A., Danner, S.A., Savelkoul, P.H., Vandenbroucke-Grauls, C.M., 2004. New developments in the diagnosis of bloodstream infections. Lancet Infect. Dis., 4(12):751–760. [doi:10.1016/S1473-3099(04)01205-8]PubMedCrossRefGoogle Scholar
  22. Schmitt, M., Bravo, I.G., Snijders, P.J., Gissmann, L., Pawlita M., Waterboer, T., 2006. Bead-based multiplex genotyping of human papillomaviruses. J. Clin. Microbiol., 44(2):504–512. [doi:10.1128/JCM.44.2.504-512.2006]PubMedCrossRefGoogle Scholar
  23. Troesch, A., Nguyen, H., Miyada, C.G., Desvarenne, S., Gingeras, T.R., Kaplan, P.M., Cros, P., Mabilat, C., 1999. Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays. J. Clin. Microbiol., 37(1):49–55.PubMedGoogle Scholar
  24. Vandamme, P., Pot, B., Gillis, M., de Vos, P., Kersters, K., Swings, J., 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev., 60(2):407–438.PubMedGoogle Scholar
  25. Wetmur, J.G., 1991. DNA probes: applications of the principles of nucleic acid hybridization. Crit. Rev. Biochem. Mol. Biol., 26(3):227–259. [doi:10.3109/10409239109114069]PubMedCrossRefGoogle Scholar
  26. Woese, C.R., 1987. Bacterial evolution. Microbiol. Rev., 51(2):221–271.PubMedGoogle Scholar
  27. Zehr, J.P., Crumbliss, L.L., Church, M.J., Omoregie, E.O., Jenkins, B.D., 2003. Nitrogenase genes in PCR and RT-PCR reagents: implications for studies of diversity of functional genes. Biotechniques, 35(5):996–1002, 1004–1005.PubMedGoogle Scholar

Copyright information

© Zhejiang University Press 2008

Authors and Affiliations

  • Xiao-li Hou
    • 1
  • Han-liang Jiang
    • 1
  • Qing-yi Cao
    • 1
  • Li-ying Zhao
    • 1
  • Barbara J. Chang
    • 2
  • Zhi Chen
    • 1
  1. 1.Institute of Infectious Diseases, the First Affiliated Hospital, School of MedicineZhejiang UniversityHangzhouChina
  2. 2.Department of Microbiology and Immunology, School of Biomedical, Biomolecular and Chemical SciencesUniversity of Western AustraliaNedlandsAustralia

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