Rapid bacterial identification using evanescent-waveguide oligonucleotide microarray classification

被引:19
作者
Francois, Patrice [1 ]
Charbonnier, Yvan
Jacquet, Jean
Utinger, Dominic
Bento, Manuela
Lew, Daniel
Kresbach, Gerhard M.
Ehrat, Markus
Schlegel, Werner
Schrenzel, Jacques
机构
[1] Univ Hosp Geneva, Gen Res Lab, Infect Dis Serv, CH-1211 Geneva 14, Switzerland
[2] Univ Hosp Geneva, Clin Microbiol Lab, Infect Dis Serv, CH-1211 Geneva 14, Switzerland
[3] Fdn Rech Med, Geneva, Switzerland
[4] Ctr Med Univ Geneva, Fac Med, Comp Unit, Geneva, Switzerland
[5] Zeptosens Div Bayer AG Schweiz, Witterswil, Switzerland
关键词
bacteria; rapid identification; microarrays; planar-waveguide; neural network;
D O I
10.1016/j.mimet.2005.08.012
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Bacterial identification relies primarily on culture-based methodologies and requires 48-72 h to deliver results. We developed and used i) a bioinformatics strategy to select oligonucleotide signature probes, ii) a rapid procedure for RNA labelling and hybridization, iii) an evanescent-waveguide oligoarray with exquisite signal/noise performance, and iv) informatics methods for microarray data analysis. Unique 19-mer signature oligonucleotides were selected in the 5'-end of 16s rDNA genes of human pathogenic bacteria. Oligonucleotides spotted onto a Ta2O5-coated microarray surface were incubated with chemically labelled total bacterial RNA. Rapid hybridization and stringent washings were performed before scanning and analyzing the slide. In the present paper, the eight most abundant bacterial pathogens representing > 54% of positive blood cultures were selected. Hierarchical clustering analysis of hybridization data revealed characteristic patterns, even for closely related species. We then evaluated artificial intelligence-based approaches that outperformed conventional threshold-based identification schemes on cognate probes. At this stage, the complete procedure applied to spiked blood cultures was completed in less than 6 It. In conclusion, when coupled to optimal signal detection strategy, microarrays provide bacterial identification within a few hours post-sampling, allowing targeted antimicrobial prescription. (c) 2005 Elsevier B.V. All rights reserved.
引用
收藏
页码:390 / 403
页数:14
相关论文
共 60 条
  • [1] Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
    Alon, U
    Barkai, N
    Notterman, DA
    Gish, K
    Ybarra, S
    Mack, D
    Levine, AJ
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 96 (12) : 6745 - 6750
  • [2] Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array
    Anthony, RM
    Brown, TJ
    French, GL
    [J]. JOURNAL OF CLINICAL MICROBIOLOGY, 2000, 38 (02) : 781 - 788
  • [3] A faithful method for PCR-mediated global mRNA amplification and its integration into microarray analysis on laser-captured cells
    Aoyagi, K
    Tatsuta, T
    Nishigaki, M
    Akimoto, S
    Tanabe, C
    Omoto, Y
    Hayashi, S
    Sakamoto, H
    Sakamoto, M
    Yoshida, T
    Terada, M
    Sasaki, H
    [J]. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2003, 300 (04) : 915 - 920
  • [4] Portable system for microbial sample preparation and oligonucleotide microarray analysis
    Bavykin, SG
    Akowski, JP
    Zakhariev, VM
    Barsky, VE
    Perov, AN
    Mirzabekov, AD
    [J]. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2001, 67 (02) : 922 - 928
  • [5] Rapid identification of Escherichia coli pathotypes by virulence gene detection with DNA microarrays
    Bekal, S
    Brousseau, R
    Masson, L
    Prefontaine, G
    Fairbrother, J
    Harel, J
    [J]. JOURNAL OF CLINICAL MICROBIOLOGY, 2003, 41 (05) : 2113 - 2125
  • [6] Berrar Daniel P, 2003, Pac Symp Biocomput, P5
  • [7] Detection of bacterial pathogens in environmental samples using DNA microarrays
    Call, DR
    Borucki, MK
    Loge, FJ
    [J]. JOURNAL OF MICROBIOLOGICAL METHODS, 2003, 53 (02) : 235 - 243
  • [8] A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus -: art. no. 95
    Charbonnier, Y
    Gettler, B
    Francois, P
    Bento, M
    Renzoni, A
    Vaudaux, P
    Schlegel, W
    Schrenzel, J
    [J]. BMC GENOMICS, 2005, 6 (1)
  • [9] Microarray analysis of microbial virulence factors
    Chizhikov, V
    Rasooly, A
    Chumakov, K
    Levy, DD
    [J]. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2001, 67 (07) : 3258 - 3263
  • [10] High-density DNA probe arrays for identification of staphylococci to the species level
    Couzinet, S
    Jay, C
    Barras, C
    Vachon, R
    Vernet, G
    Ninet, B
    Jane, I
    Minazio, MA
    Francois, P
    Lew, D
    Troesch, A
    Schrenzel, J
    [J]. JOURNAL OF MICROBIOLOGICAL METHODS, 2005, 61 (02) : 201 - 208