Full Text:   <2812>

CLC number: R37

On-line Access: 

Received: 2007-09-05

Revision Accepted: 2008-02-19

Crosschecked: 0000-00-00

Cited: 5

Clicked: 5330

Citations:  Bibtex RefMan EndNote GB/T7714

-   Go to

Article info.
1. Reference List
Open peer comments

Journal of Zhejiang University SCIENCE B 2008 Vol.9 No.4 P.291-298

http://doi.org/10.1631/jzus.B0710470


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


Author(s):  Xiao-li HOU, Han-liang JIANG, Qing-yi CAO, Li-ying ZHAO, Barbara J. CHANG, Zhi CHEN

Affiliation(s):  Institute of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; more

Corresponding email(s):   chenzhi@zju.edu.cn

Key Words:  Oligonucleotide array, Bacteremia, 23S rRNA, Multiplexed detection


Xiao-li HOU, Han-liang JIANG, Qing-yi CAO, Li-ying ZHAO, Barbara J. CHANG, Zhi CHEN. Using oligonucleotide suspension arrays for laboratory identification of bacteria responsible for bacteremia[J]. Journal of Zhejiang University Science B, 2008, 9(4): 291-298.

@article{title="Using oligonucleotide suspension arrays for laboratory identification of bacteria responsible for bacteremia",
author="Xiao-li HOU, Han-liang JIANG, Qing-yi CAO, Li-ying ZHAO, Barbara J. CHANG, Zhi CHEN",
journal="Journal of Zhejiang University Science B",
volume="9",
number="4",
pages="291-298",
year="2008",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.B0710470"
}

%0 Journal Article
%T Using oligonucleotide suspension arrays for laboratory identification of bacteria responsible for bacteremia
%A Xiao-li HOU
%A Han-liang JIANG
%A Qing-yi CAO
%A Li-ying ZHAO
%A Barbara J. CHANG
%A Zhi CHEN
%J Journal of Zhejiang University SCIENCE B
%V 9
%N 4
%P 291-298
%@ 1673-1581
%D 2008
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B0710470

TY - JOUR
T1 - Using oligonucleotide suspension arrays for laboratory identification of bacteria responsible for bacteremia
A1 - Xiao-li HOU
A1 - Han-liang JIANG
A1 - Qing-yi CAO
A1 - Li-ying ZHAO
A1 - Barbara J. CHANG
A1 - Zhi CHEN
J0 - Journal of Zhejiang University Science B
VL - 9
IS - 4
SP - 291
EP - 298
%@ 1673-1581
Y1 - 2008
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B0710470


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.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

Reference

[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.

[2] Armstrong, B., Stewart, M., Mazumder, A., 2000. Suspension arrays for high throughput, multiplexed single nucleotide polymorphism genotyping. Cytometry, 40(2):102-108.

[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.

[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.

[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.

[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.

[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.

[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.

[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).

[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.

[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.

[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.

[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.

[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.

[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.

[16] Kwok, S., Higuchi, R., 1989. Avoiding false positives with PCR. Nature, 339(6221):237-238.

[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.

[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.

[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.

[20] Nolan, J.P., Sklar, L.A., 2002. Suspension array technology: evolution of the flat-array paradigm. Trends Biotechnol., 20(1):9-12.

[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.

[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.

[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.

[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.

[25] Wetmur, J.G., 1991. DNA probes: applications of the principles of nucleic acid hybridization. Crit. Rev. Biochem. Mol. Biol., 26(3):227-259.

[26] Woese, C.R., 1987. Bacterial evolution. Microbiol. Rev., 51(2):221-271.

[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.

Open peer comments: Debate/Discuss/Question/Opinion

<1>

Please provide your name, email address and a comment





Journal of Zhejiang University-SCIENCE, 38 Zheda Road, Hangzhou 310027, China
Tel: +86-571-87952783; E-mail: cjzhang@zju.edu.cn
Copyright © 2000 - 2022 Journal of Zhejiang University-SCIENCE