Oligonucleotide and DNA Microarrays: Versatile Tools for Rapid Bacterial Diagnostics

  • Tanja Kostic
  • Patrice Francois
  • Levente Bodrossy
  • Jacques Schrenzel


The rapid and unambiguous detection and identification of microorganisms, historically a major challenge of clinical microbiology, gained additional importance in the fields of public health and biodefence. These requirements cannot be well addressed by classical culture-based approaches. Therefore, a wide range of molecular approaches has been suggested. Microarrays are molecular tools that can be used for simultaneous identification of microorganisms in clinical and environmental samples. Main advantages of microarrays are high throughput, parallelism and miniaturization of the detection system. Furthermore, they allow for both high specificity and high sensitivity of the detection.

Microarrays consist of set of probes immobilized on a solid surface. Even though the first application of the microarrays can be seen as relatively recent (Schena et al. 1995), the technology developed rapidly reaching the milestone of 5,000 published papers in 2004 (Holzman and Kolker 2004). This development encompasses both the successful transfer of various technological aspects as well as the expansion of the application scope. The most important technological elements of custom-made platforms as well as the characteristics of the commercially available formats are reviewed in this chapter. Furthermore, application potential is presented together with considerations about quality control.


Oligonucleotide Microarrays Oligonucleotide Array Resonance Light Scattering Massively Parallel Signature Sequencing Appl Environ 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. Adamczyk J, Hesselsoe M, Iversen N, Horn M, Lehner A, Nielsen PH, Schloter M, Roslev P, Wagner M (2003) The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl Environ Microbiol 69:6875–6887CrossRefGoogle Scholar
  2. Ahn HJ, La HJ, Forney LJ (2006) System for determining the relative fitness of multiple bacterial populations without using selective markers. Appl Environ Microbiol 72:7383–7385CrossRefGoogle Scholar
  3. Aitman TJ (2001) DNA microarrays in medical practice. BMJ 323:611–615CrossRefGoogle Scholar
  4. Albert TJ, Norton J, Ott M, Richmond T, Nuwaysir K, Nuwaysir EF, Stengele KP, Green RD (2003) Light-directed 5 → 3 synthesis of complex oligonucleotide microarrays. Nucleic Acids Res 31:e35CrossRefGoogle Scholar
  5. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Staudt LM (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403:503–511CrossRefGoogle Scholar
  6. Allawi HT, SantaLucia J Jr (1998) Nearest-neighbor thermodynamics of internal AC mismatches in DNA: sequence dependence and pH effects. Biochemistry 37:9435–9444CrossRefGoogle Scholar
  7. Anthony RM, Brown TJ, French GL (2000) Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array. J Clin Microbiol 38:781–788Google Scholar
  8. Aoyagi K, Tatsuta T, Nishigaki M, Akimoto S, Tanabe C, Omoto Y, Hayashi S, Sakamoto H, Sakamoto M, Yoshida T, Terada M, Sasaki H (2003) A faithful method for PCR-mediated global mRNA amplification and its integration into microarray analysis on laser-captured cells. Biochem Biophys Res Commun 300:915–920CrossRefGoogle Scholar
  9. Armitage BA (2003) The impact of nucleic acid secondary structure on PNA hybridization. Drug Discov Today 8:222–228CrossRefGoogle Scholar
  10. Bae JW, Rhee SK, Nam YD, Park YH (2005) Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization as microarray probes. Nucleic Acids Res 33:e113CrossRefGoogle Scholar
  11. Bailly X, Bena G, Lenief V, de Lajudie P, Avarre JC (2006) Development of a lab-made microarray for analyzing the genetic diversity of nitrogen fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae. J Microbiol Methods 67:114–124CrossRefGoogle Scholar
  12. Bains W, Smith GC (1988) A novel method for nucleic acid sequence determination. J Theor Biol 135:303–307CrossRefGoogle Scholar
  13. Baldeschwieler JD, Gamble RC, Thierault TP (1995) Method and apparatus for performing multiple sequential reactions on a matrix. WO9525116, USA, Ref Type: PatentGoogle Scholar
  14. Ballmer K, Korczak BM, Kuhnert P, Slickers P, Ehricht R, Hachler H (2007) Fast DNA-serotyping of Escherichia coli by oligonucleotide microarray. J Clin Microbiol 45:370–379CrossRefGoogle Scholar
  15. Barczak A, Rodriguez MW, Hanspers K, Koth LL, Tai YC, Bolstad BM, Speed TP, Erle DJ (2003) Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res 13:1775–1785CrossRefGoogle Scholar
  16. Bavykin SG, Akowski JP, Zakhariev VM, Barsky VE, Perov AN, Mirzabekov AD (2001) Portable system for microbial sample preparation and oligonucleotide microarray analysis. Appl Environ Microbiol 67:922–928CrossRefGoogle Scholar
  17. Bekal S, Brousseau R, Masson L, Prefontaine G, Fairbrother J, Harel J (2003) Rapid identification of Escherichia coli pathotypes by virulence gene detection with DNA microarrays. J Clin Microbiol 41:2113–2125CrossRefGoogle Scholar
  18. Blanchard AP, Friend SH (1999) Cheap DNA arrays—it’s not all smoke and mirrors. Nat Biotechnol 17:953CrossRefGoogle Scholar
  19. Blanchard AP, Kaiser RJ, Hood LE (1996) High-density oligonucleotide arrays. Biosensors & Bioelectronics 11:687–690CrossRefGoogle Scholar
  20. Bo T, Jonassen I (2002) New feature subset selection procedures for classification of expression profiles. Genome Biol 3:RESEARCH0017Google Scholar
  21. Bodrossy L (2003) Diagnostic oligonucleotide microarrays for microbiology. In: Blalock E (ed) A Beginner’s Guide to Microarrays, Kluwer Academic Publishers, New York, pp 43–92Google Scholar
  22. Bodrossy L, Sessitsch A (2004) Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol 7:245–254CrossRefGoogle Scholar
  23. Bodrossy L, Stralis-Pavese N, Konrad-Koszler M, Weilharter A, Reichenauer TG, Schofer D, Sessitsch A (2006) mRNA-based parallel detection of active methanotroph populations by use of a diagnostic microarray. Appl Environ Microbiol 72:1672–1676CrossRefGoogle Scholar
  24. Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A, Sessitsch A (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5:566–582CrossRefGoogle Scholar
  25. Boldrick JC, Alizadeh AA, Diehn M, Dudoit S, Liu CL, Belcher CE, Botstein D, Staudt L, Brown PO, Relman DA (2002) Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci U S A 99:972–977CrossRefGoogle Scholar
  26. Borucki MK, Krug MJ, Muraoka WT, Call DR (2003) Discrimination among Listeria monocytogenes isolates using a mixed genome DNA microarray. Vet Microbiol 92:351–362CrossRefGoogle Scholar
  27. Borucki MK, Reynolds J, Call DR, Ward TJ, Page B, Kadushin J (2005) Suspension microarray with dendrimer signal amplification allows direct and high-throughput subtyping of Listeria monocytogenes from genomic DNA. J Clin Microbiol 43:3255–3259CrossRefGoogle Scholar
  28. Brennan TM, Heinecker H (1995) Methods and compositions for determining the sequence of nucleic acids. 5474796, USA, Ref Type: PatentGoogle Scholar
  29. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, Roth R, George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J, Fearon K, Mao J, Corcoran K (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18:630–634CrossRefGoogle Scholar
  30. Brodie EL, DeSantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL, Hazen TC, Richardson PM, Herman DJ, Tokunaga TK, Wan JM, Firestone MK (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72:6288–6298CrossRefGoogle Scholar
  31. Call DR, Bakko MK, Krug MJ, Roberts MC (2003) Identifying antimicrobial resistance genes with DNA microarrays. Antimicrob Agents Chemother 47:3290–3295CrossRefGoogle Scholar
  32. Call DR, Borucki MK, Loge FJ (2003) Detection of bacterial pathogens in environmental samples using DNA microarrays. J Microbiol Methods 53:235–243CrossRefGoogle Scholar
  33. Case-Green SC, Southern EM (1994) Studies on the base pairing properties of deoxyinosine by solid phase hybridisation to oligonucleotides. Nucleic Acids Res 22:131–136CrossRefGoogle Scholar
  34. Cassat JE, Dunman PM, McAleese F, Murphy E, Projan SJ, Smeltzer MS (2005) Comparative genomics of Staphylococcus aureus musculoskeletal isolates. J Bacteriol 187:576–592CrossRefGoogle Scholar
  35. Charbonnier Y, Gettler BM, Francois P, Bento M, Renzoni A, Vaudaux P, Schlegel W, Schrenzel J (2005) A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus. BMC Genomics 6:95CrossRefGoogle Scholar
  36. Chizhikov V, Rasooly A, Chumakov K, Levy DD (2001) Microarray analysis of microbial virulence factors. Appl Environ Microbiol 67:3258–3263CrossRefGoogle Scholar
  37. Couzinet S, Jay C, Barras C, Vachon R, Vernet G, Ninet B, Jan I, Minazio MA, Francois P, Lew D, Troesch A, Schrenzel J (2005a) High-density DNA probe arrays for identification of staphylococci to the species level. J Microbiol Methods 61:201–208CrossRefGoogle Scholar
  38. Couzinet S, Yugueros J, Barras C, Visomblin N, Francois P, Lacroix B, Vernet G, Lew D, Troesch A, Schrenzel J, Jay C (2005b) Evaluation of a high-density oligonucleotide array for characterization of grlA, grlB, gyrA and gyrB mutations in fluoroquinolone resistant Staphylococcus aureus isolates. J Microbiol Methods 60:275–279CrossRefGoogle Scholar
  39. Debouck C, Goodfellow PN 1999 DNA microarrays in drug discovery and development. Nat Genet 21:48–50Google Scholar
  40. Denef VJ, Park J, Rodrigues JL, Tsoi TV, Hashsham SA, Tiedje JM (2003) Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ Microbiol 5:933–943CrossRefGoogle Scholar
  41. Diehl F, Grahlmann S, Beier M, Hoheisel JD (2001) Manufacturing DNA microarrays of high spot homogeneity and reduced background signal. Nucleic Acids Res 29:E38CrossRefGoogle Scholar
  42. Dorrell N, Hinchliffe SJ, Wren BW (2005) Comparative phylogenomics of pathogenic bacteria by microarray analysis. Curr Opin Microbiol 8:620–626CrossRefGoogle Scholar
  43. Drmanac R, Crkvenjakov R (1993) Method of sequencing of genomes by hybridization of oligonucleotide probes. US1991000723712 USA, Ref Type: PatentGoogle Scholar
  44. Drmanac R, Drmanac S (1999) cDNA screening by array hybridization. Methods Enzymol 303:165–78CrossRefGoogle Scholar
  45. Drmanac R, Drmanac S, Strezoska Z, Paunesku T, Labat I, Zeremski M, Snoddy J, Funkhouser WK, Koop B, Hood L (1993) DNA sequence determination by hybridization: a strategy for efficient large-scale sequencing. Science 260:1649–1652CrossRefGoogle Scholar
  46. Drmanac S, Kita D, Labat I, Hauser B, Schmidt C, Burczak JD, Drmanac R (1998) Accurate sequencing by hybridization for DNA diagnostics and individual genomics. Nat Biotechnol 16:54–58CrossRefGoogle Scholar
  47. Dunbar SA, Vander Zee CA, Oliver KG, Karem KL, Jacobson JW (2003) Quantitative, multiplexed detection of bacterial pathogens: DNA and protein applications of the Luminex LabMAP system. J Microbiol Methods 53:245–252CrossRefGoogle Scholar
  48. Duveneck GL, Bopp MA, Ehrat M, Balet LP, Haiml M, Keller U, Marowsky G, Soria S (2003) Two-photon fluorescence excitation of macroscopic areas on planar waveguides. Biosens Bioelectron 18:503–510CrossRefGoogle Scholar
  49. Epstein JR, Ferguson JA, Lee KH, Walt DR (2003a) Combinatorial decoding: an approach for universal DNA array fabrication. J Am Chem Soc 125:13753–13759CrossRefGoogle Scholar
  50. Epstein JR, Leung AP, Lee KH, Walt DR (2003b) High-density, microsphere-based fiber optic DNA microarrays. Biosens Bioelectron 18:541–546CrossRefGoogle Scholar
  51. Epstein JR, Walt DR (2003) Fluorescence-based fibre optic arrays: a universal platform for sensing. Chem Soc Rev 32:203–214CrossRefGoogle Scholar
  52. Ericsson O, Sivertsson A, Lundeberg J, Ahmadian A (2003) Microarray-based resequencing by apyrase-mediated allele-specific extension. Electrophoresis 24:3330–3338CrossRefGoogle Scholar
  53. Fan J, Chen Y, Chan HM, Tam PK, Ren Y (2005) Removing intensity effects and identifying significant genes for Affymetrix arrays in macrophage migration inhibitory factor-suppressed neuroblastoma cells. Proc Natl Acad Sci U S A 102:17751–17756CrossRefGoogle Scholar
  54. Fan J, Tam P, Woude GV, Ren Y (2004) Normalization and analysis of cDNA microarrays using within-array replications applied to neuroblastoma cell response to a cytokine. Proc Natl Acad Sci U S A 101:1135–1140CrossRefGoogle Scholar
  55. Fan JB, Chen X, Halushka MK, Berno A, Huang X, Ryder T, Lipshutz RJ, Lockhart DJ, Chakravarti A (2000) Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res 10:853–860CrossRefGoogle Scholar
  56. Ferguson JA, Steemers FJ, Walt DR (2000) High-density fiber-optic DNA random microsphere array. Anal Chem 72:5618–5624Google Scholar
  57. Fodor SP, Rava RP, Huang XC, Pease AC, Holmes CP, Adams CL (1993) Multiplexed biochemical assays with biological chips. Nature 364:555–556CrossRefGoogle Scholar
  58. Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D (1991) Light-directed, spatially addressable parallel chemical synthesis. Science 251:767–773CrossRefGoogle Scholar
  59. Francois P, Bento M, Vaudaux P, Schrenzel J (2003) Comparison of fluorescence and resonance light scattering for highly sensitive microarray detection of bacterial pathogens. J Microbiol Methods 55:755–762CrossRefGoogle Scholar
  60. Francois P, Charbonnier Y, Jaquet J, Utinger D, Bento M, Lew DP, Kresbach G, Schlegel W, Schrenzel J (2005) Rapid bacterial identification using evanescent waveguide oligonucleotide microarray classification. J Microbiol Methods 65:390–403CrossRefGoogle Scholar
  61. Francois P, Garzoni C, Bento M, Schrenzel J (2007) Comparison of amplification methods for transcriptomic analysis of low abundance prokaryotic RNA sources. J Microbiol Methods 68(2):385–91CrossRefGoogle Scholar
  62. Franke-Whittle IH, Klammer SH, Mayrhofer S, Insam H (2006) Comparison of different labeling methods for the production of labeled target DNA for microarray hybridization. J Microbiol Methods 65:117–126CrossRefGoogle Scholar
  63. Fredericks DN, Relman DA (1996) Sequence-based identification of microbial pathogens: a reconsideration of Koch’s postulates. Clin Microbiol Rev 9:18–33Google Scholar
  64. Garaizar J, Rementeria A, Porwollik S (2006) DNA microarray technology: a new tool for the epidemiological typing of bacterial pathogens? FEMS Immunol Med Microbiol 47:178–189CrossRefGoogle Scholar
  65. Garzoni C, Francois P, Couzinet S, Tapparel C, Charbonnier Y, Huyghe A, Renzoni A, Lucchini S, Lew DP, Vaudaux P,Kelley WL, Schrenzel J (2007) A global view of the Staphylococcus aureus whole genome expression upon internalization in human epithelial cells, BMC Genomics 14:171CrossRefGoogle Scholar
  66. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11:4241–4257Google Scholar
  67. Gill RT, Katsoulakis E, Schmitt W, Taroncher-Oldenburg G, Misra J, Stephanopoulos G (2002) Genome-wide dynamic transcriptional profiling of the light-to-dark transition in Synechocystis sp strain PCC 6803. J Bacteriol 184:3671–3681CrossRefGoogle Scholar
  68. Gillepsie D, Spiegelman SA (1965) A quantitative assay for DNA-RNA hybrids with DNA immobilized on a membrane. J Mol Biol 12:829–842CrossRefGoogle Scholar
  69. Gingeras TR, Ghandour G, Wang E, Berno A, Small PM, Drobniewski F, Alland D, Desmond E, Holodniy M, Drenkow J (1998) Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. Genome Res 8:435–448Google Scholar
  70. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286:531–537CrossRefGoogle Scholar
  71. Grifantini R, Bartolini E, Muzzi A, Draghi M, Frigimelica E, Berger J, Ratti G, Petracca R, Galli G, Agnusdei M, Giuliani MM, Santini L, Brunelli B, Tettelin H, Rappuoli R, Randazzo F, Grandi G (2002) Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays. Nat Biotechnol 20:914–921CrossRefGoogle Scholar
  72. Guschin D, Yershov G, Zaslavsky A, Gemmell A, Shick V, Proudnikov D, Arenkov P, Mirzabekov A (1997) Manual manufacturing of oligonucleotide, DNA, and protein microchips. Anal Biochem 250:203–211CrossRefGoogle Scholar
  73. Hacia JG (1999) Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet 21:42–47CrossRefGoogle Scholar
  74. Halperin A, Buhot A, Zhulina EB (2005) Brush effects on DNA chips: thermodynamics, kinetics, and design guidelines. Biophys J 89:796–811CrossRefGoogle Scholar
  75. Hardenbol P, Baner J, Jain M, Nilsson M, Namsaraev EA, Karlin-Neumann GA, Fakhrai-Rad H, Ronaghi M, Willis TD, Landegren U, Davis RW (2003) Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat Biotechnol 21:673–678CrossRefGoogle Scholar
  76. Hardenbol P, Yu F, Belmont J, Mackenzie J, Bruckner C, Brundage T, Boudreau A, Chow S, Eberle J, Erbilgin A,Falkowski M, Fitzgerald R, Ghose S, Iartchouk O, Jain M, Karlin-Neumann G, Lu X, Miao X, Moore B,Moorhead M, Namsaraev E, Pasternak S, Prakash E, Tran K, Wang Z, Jones HB, Davis RW, Willis TD, Gibbs RA (2005) Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res 15:269–275CrossRefGoogle Scholar
  77. Hashsham SA, Wick LM, Rouillard JM, Gulari E, Tiedje JM (2004) Potential of DNA microarrays for developing parallel detection tools (PDTs) for microorganisms relevant to biodefense and related research needs. Biosens Bioelectron 20:668–683CrossRefGoogle Scholar
  78. Hessner MJ, Meyer L, Tackes J, Muheisen S, Wang X (2004) Immobilized probe and glass surface chemistry as variables in microarray fabrication. BMC Genomics 5:53CrossRefGoogle Scholar
  79. Holzman T, Kolker E (2004) Statistical analysis of global gene expression data: some practical considerations. Curr Opin Biotechnol 15:52–57CrossRefGoogle Scholar
  80. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Ziman M, Meyer MR, Kobayashi S, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19:342–347CrossRefGoogle Scholar
  81. Jaeger J, Spang R (2006) Selecting normalization genes for small diagnostic microarrays. BMC Bioinformatics 7:388CrossRefGoogle Scholar
  82. Joyce EA, Chan K, Salama NR, Falkow S (2002) Redefining bacterial populations: a post-genomic reformation. Nat Rev Genet 3:462–473Google Scholar
  83. Kafatos FC, Jones CW, Efstratiadis A (1979) Determination of nucleic acid sequence homologies and relative concentrations by a dot hybridization procedure. Nucleic Acids Res 7:1541–1552CrossRefGoogle Scholar
  84. Kajiyama T, Miyahara Y, Kricka LJ, Wilding P, Graves DJ, Surrey S, Fortina P (2003) Genotyping on a thermal gradient DNA chip. Genome Res 13:467–475CrossRefGoogle Scholar
  85. Kakinuma K, Fukushima M, Kawaguchi R (2003) Detection and identification of Escherichia coli, Shigella, and Salmonella by microarrays using the gyrB gene. Biotechnol Bioeng 83:721–728CrossRefGoogle Scholar
  86. Kelly JJ, Chernov BK, Tovstanovsky I, Mirzabekov AD, Bavykin SG (2002) Radical-generating coordination complexes as tools for rapid and effective fragmentation and fluorescent labeling of nucleic acids for microchip hybridization. Anal Biochem 311:103–118CrossRefGoogle Scholar
  87. Kessler N, Ferraris O, Palmer K, Marsh W, Steel A (2004) Use of the DNA flow-thru chip, a three-dimensional biochip, for typing and subtyping of influenza viruses. J Clin Microbiol 42:2173–2185CrossRefGoogle Scholar
  88. Knight J (2001) When the chips are down. Nature 410:860–861CrossRefGoogle Scholar
  89. Koessler T, Francois P, Charbonnier Y, Huyghe A, Bento M, Dharan S, Renzi G, Lew D, Harbarth S, Pittet D, Schrenzel J (2006) Use of oligoarrays for characterization of community-onset methicillin-resistant Staphylococcus aureus. J Clin Microbiol 44:1040–1048CrossRefGoogle Scholar
  90. Korczak B, Frey J, Schrenzel J, Pluschke G, Pfister R, Ehricht R, Kuhnert P (2005) Use of diagnostic microarrays for determination of virulence gene patterns of Escherichia coli K1, a major cause of neonatal meningitis. J Clin Microbiol 43:1024–1031CrossRefGoogle Scholar
  91. Kostic T, Weilharter A, Rubino S, Delogu G, Rudi K, Sessitsch A, Bodrossy L (2007) A microbial diagnostic microarray technique for the detection and identification of pathogenic bacteria in a background of non-pathogens. Anal Biochem 360:244–254CrossRefGoogle Scholar
  92. Kothapalli R, Yoder SJ, Mane S, Loughran TP Jr (2002) Microarray results: how accurate are they? BMC Bioinformatics 3:22CrossRefGoogle Scholar
  93. Kroll TC, Wolfl S (2002) Ranking: a closer look on globalisation methods for normalisation of gene expression arrays. Nucleic Acids Res 30:e50CrossRefGoogle Scholar
  94. Li J, Pankratz M, Johnson JA (2002) Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays. Toxicol Sci 69:383–390CrossRefGoogle Scholar
  95. Li W (2005) How many genes are needed for early detection of breast cancer, based on gene expression patterns in peripheral blood cells? Breast Cancer Res 7:E5CrossRefGoogle Scholar
  96. Lima WF, Monia BP, Ecker DJ, Freier SM (1992) Implication of RNA structure on antisense oligonucleotide hybridization kinetics. Biochemistry 31:12055–12061CrossRefGoogle Scholar
  97. Lindroos HL, Mira A, Repsilber D, Vinnere O, Naslund K, Dehio M, Dehio C, Andersson SG (2005) Characterization of the genome composition of Bartonella koehlerae by microarray comparative genomic hybridization profiling. J Bacteriol 187:6155–6165CrossRefGoogle Scholar
  98. Lindroos K, Liljedahl U, Raitio M, Syvanen AC (2001) Minisequencing on oligonucleotide microarrays: comparison of immobilisation chemistries. Nucleic Acids Res 29:E69CrossRefGoogle Scholar
  99. Lindroos K, Sigurdsson S, Johansson K, Ronnblom L, Syvanen AC (2002) Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system. Nucleic Acids Res 30:e70CrossRefGoogle Scholar
  100. Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ (1999) High density synthetic oligonucleotide arrays. Nat Genet 21:20–24CrossRefGoogle Scholar
  101. Lipshutz RJ, Morris D, Chee M, Hubbell E, Kozal MJ, Shah N, Shen N, Yang R, Fodor SP (1995) Using oligonucleotide probe arrays to access genetic diversity. Biotechniques 19:442–447Google Scholar
  102. Liu M, Popper SJ, Rubins KH, Relman DA (2006) Early days: genomics and human responses to infection. Curr Opin Microbiol 9:312–319CrossRefGoogle Scholar
  103. Liu WT, Guo H, Wu JH (2007) Effects of target length on the hybridization efficiency and specificity of rRNA-based oligonucleotide microarrays. Appl Environ Microbiol 73:73–82CrossRefGoogle Scholar
  104. Liu WT, Mirzabekov AD, Stahl DA (2001) Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ Microbiol 3:619–629CrossRefGoogle Scholar
  105. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14:1675–1680CrossRefGoogle Scholar
  106. Lodes MJ, Suciu D, Elliott M, Stover AG, Ross M, Caraballo M, Dix K, Crye J, Webby RJ, Lyon WJ, Danley DL,McShea A (2006) Use of semiconductor-based oligonucleotide microarrays for influenza A virus subtype identification and sequencing. J Clin Microbiol 44:1209–1218CrossRefGoogle Scholar
  107. Loge FJ, Thompson DE, Call DR (2002) PCR detection of specific pathogens in water: a risk-based analysis. Environ Sci Technol 36:2754–2759CrossRefGoogle Scholar
  108. Loy A, Bodrossy L (2006) Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin Chim Acta 363:106–119CrossRefGoogle Scholar
  109. Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer KH, Wagner M (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68:5064–5081CrossRefGoogle Scholar
  110. Loy A, Schulz C, Lucker S, Schopfer-Wendels A, Stoecker K, Baranyi C, Lehner A, Wagner M (2005) 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales." Appl Environ Microbiol 71:1373–1386CrossRefGoogle Scholar
  111. Lucchini S, Liu H, Jin Q, Hinton JC, Yu J (2005) Transcriptional adaptation of Shigella flexneri during infection of macrophages and epithelial cells: insights into the strategies of a cytosolic bacterial pathogen. Infect Immun 73:88–102CrossRefGoogle Scholar
  112. Lucchini S, Thompson A, Hinton JC (2001) Microarrays for microbiologists. Microbiology 147:1403–1414Google Scholar
  113. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, Buchner A, Lai T, Steppi S, Jobb G, Forster W,Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Konig A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A,Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371CrossRefGoogle Scholar
  114. Lynch JL, deSilva CJ, Peeva VK, Swanson NR (2006) Comparison of commercial probe labeling kits for microarray: towards quality assurance and consistency of reactions. Anal Biochem 355:224–231Google Scholar
  115. Macevicz SC (1991) Nucleic acid sequence determination by multiple mixed oligonucleotide probes. US1988000261702 USA Ref Type: PatentGoogle Scholar
  116. Malanoski GJ, Samore MH, Pefanis A, Karchmer AW (1995) Staphylococcus aureus catheter-associated bacteremia. Minimal effective therapy and unusual infectious complications associated with arterial sheath catheters. Arch Intern Med 155:1161–1166CrossRefGoogle Scholar
  117. Marcelino LA, Backman V, Donaldson A, Steadman C, Thompson JR, Preheim SP, Lien C, Lim E, Veneziano D, Polz MF (2006) Accurately quantifying low-abundant targets amid similar sequences by revealing hidden correlations in oligonucleotide microarray data. Proc Natl Acad Sci U S A 103:13629–13634CrossRefGoogle Scholar
  118. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ,Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC,Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP,Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA,Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380Google Scholar
  119. Maskos U, Southern EM (1993a) A novel method for the parallel analysis of multiple mutations in multiple samples. Nucleic Acids Res 21:2269–2270CrossRefGoogle Scholar
  120. Maskos U, Southern EM (1993b) A study of oligonucleotide reassociation using large arrays of oligonucleotides synthesised on a glass support. Nucleic Acids Res 21:4663–4669CrossRefGoogle Scholar
  121. Matveeva OV, Shabalina SA, Nemtsov VA, Tsodikov AD, Gesteland RF, Atkins JF (2003) Thermodynamic calculations and statistical correlations for oligo-probes design. Nucleic Acids Res 31:4211–4217CrossRefGoogle Scholar
  122. Mikulowska-Mennis A, Taylor TB, Vishnu P, Michie SA, Raja R, Horner N, Kunitake ST (2002) High-quality RNA from cells isolated by laser capture microdissection. Biotechniques 33:176–179Google Scholar
  123. Mir KU, Southern EM (1999) Determining the influence of structure on hybridization using oligonucleotide arrays. Nat Biotechnol 17:788–792CrossRefGoogle Scholar
  124. Murray AE, Lies D, Li G, Nealson K, Zhou J, Tiedje JM (2001) DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. Proc Natl Acad Sci U S A 98:9853–9858CrossRefGoogle Scholar
  125. Naef F, Magnasco MO (2003) Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays. Phys Rev E Stat Nonlin Soft Matter Phys 68:011906Google Scholar
  126. Nguyen HK, Southern EM (2000) Minimising the secondary structure of DNA targets by incorporation of a modified deoxynucleoside: implications for nucleic acid analysis by hybridisation. Nucleic Acids Res 28:3904–3909CrossRefGoogle Scholar
  127. Pasternack RF, Collings PJ (1995) Resonance light scattering: a new technique for studying chromophore aggregation. Science 269:935–939CrossRefGoogle Scholar
  128. Pawlak M, Schick E, Bopp MA, Schneider MJ, Oroszlan P, Ehrat M (2002) Zeptosens’ protein microarrays: a novel high performance microarray platform for low abundance protein analysis. Proteomics 2:383–393CrossRefGoogle Scholar
  129. Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, Fodor SP (1994) Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci U S A 91:5022–5026CrossRefGoogle Scholar
  130. Peplies J, Glockner FO, Amann R (2003) Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl Environ Microbiol 69:1397–1407CrossRefGoogle Scholar
  131. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lonning PE, Borresen-Dale AL, Brown PO, Botstein D (2000) Molecular portraits of human breast tumours. Nature 406:747–752Google Scholar
  132. Perreten V, Vorlet-Fawer L, Slickers P, Ehricht R, Kuhnert P, Frey J (2005) Microarray-based detection of 90 antibiotic resistance genes of gram-positive bacteria. J Clin Microbiol 43:2291–2302CrossRefGoogle Scholar
  133. Peterson AW, Heaton RJ, Georgiadis RM (2001) The effect of surface probe density on DNA hybridization. Nucleic Acids Res 29:5163–5168CrossRefGoogle Scholar
  134. Phimister B (1999) Chipping forecast: going global. Nat Genet 21 Suppl:1Google Scholar
  135. Porwollik S, Frye J, Florea LD, Blackmer F, McClelland M (2003) A non-redundant microarray of genes for two related bacteria. Nucleic Acids Res 31:1869–1876CrossRefGoogle Scholar
  136. Pozhitkov A, Chernov B, Yershov G, Noble PA (2005) Evaluation of gel-pad oligonucleotide microarray technology by using artificial neural networks. Appl Environ Microbiol 71:8663–8676CrossRefGoogle Scholar
  137. Pozhitkov A, Noble PA, Domazet-Loso T, Nolte AW, Sonnenberg R, Staehler P, Beier M, Tautz D (2006) Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Res 34:e66CrossRefGoogle Scholar
  138. Proudnikov D, Mirzabekov A (1996) Chemical methods of DNA and RNA fluorescent labeling. Nucleic Acids Res 24:4535–4542CrossRefGoogle Scholar
  139. Puskas LG, Zvara A, Hackler L Jr, Van Hummelen P (2002) RNA amplification results in reproducible microarray data with slight ratio bias. Biotechniques 32:1330–4, 1336, 1338, 1340Google Scholar
  140. Raman R, Raguram S, Venkataraman G, Paulson JC, Sasisekharan R (2005) Glycomics: an integrated systems approach to structure-function relationships of glycans. Nat Methods 2:817–824CrossRefGoogle Scholar
  141. Rhee SK, Liu X, Wu L, Chong SC, Wan X, Zhou J (2004) Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol 70:4303–4317CrossRefGoogle Scholar
  142. Rimour S, Hill D, Militon C, Peyret P (2005) GoArrays: highly dynamic and efficient microarray probe design. Bioinformatics 21:1094–1103CrossRefGoogle Scholar
  143. Roth FP, Hughes JD, Estep PW, Church GM (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol 16:939–945CrossRefGoogle Scholar
  144. Rudi K, Flateland SL, Hanssen JF, Bengtsson G, Nissen H (2002) Development and evaluation of a 16S ribosomal DNA array-based approach for describing complex microbial communities in ready-to-eat vegetable salads packed in a modified atmosphere. Appl Environ Microbiol 68:1146–1156CrossRefGoogle Scholar
  145. Rudi K, Treimo J, Nissen H, Vegarud G (2003) Protocols for 16S rDNA array analyses of microbial communities by sequence-specific labeling of DNA probes. ScientificWorldJournal 3:578–584CrossRefGoogle Scholar
  146. Salama N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, Falkow S (2000) A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci U S A 97:14668–14673CrossRefGoogle Scholar
  147. Sanguin H, Herrera A, Oger-Desfeux C, Dechesne A, Simonet P, Navarro E, Vogel T M, Moenne-Loccoz Y, Nesme X,Grundmann GL (2006) Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria. Environ Microbiol 8:289–307CrossRefGoogle Scholar
  148. SantaLucia J Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A 95:1460–1465CrossRefGoogle Scholar
  149. SantaLucia JJ, Allawi HT, Seneviratne PA (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35:3555–3562CrossRefGoogle Scholar
  150. Santos SR, Ochman H (2004) Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol 6:754–759CrossRefGoogle Scholar
  151. Schadt EE, Li C, Ellis B, Wong WH (2001) Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J Cell Biochem Suppl Suppl 37:120–125Google Scholar
  152. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470CrossRefGoogle Scholar
  153. Scherl A, Francois P, Charbonnier Y, Deshusses JM, Koessler T, Huyghe A, Bento M, Stahl-Zeng J, Fischer A, Masselot A, Gallé F, Renzoni A, Vaudaux P, Lew D, Zimmermann-Ivol CG, Binz PA, Sanchez JC, Hochstrasser DF,Schrenzel J (2006) Exploring glycopeptide resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance related markers. BMC Genomics 7:-296Google Scholar
  154. Schrenzel J, Hibbs J (2003) Non-cognate hybridization system (NCHS). 00/75377 A2 Ref Type: PatentGoogle Scholar
  155. Sergeev N, Distler M, Courtney S, Al Khaldi SF, Volokhov D, Chizhikov V, Rasooly A (2004) Multipathogen oligonucleotide microarray for environmental and biodefense applications. Biosens Bioelectron 20:684–698CrossRefGoogle Scholar
  156. Shchepinov MS, Case-Green SC, Southern EM (1997) Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res 25:1155–1161CrossRefGoogle Scholar
  157. Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, De Longueville F, Kawasaki ES, Lee KY,Luo Y, Sun YA, Willey JM, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM,Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M,Wolber PK, Zhang L, Slikker W Jr, Shi L, Reid LH (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24:1151–1161Google Scholar
  158. Small J, Call DR, Brockman FJ, Straub TM, Chandler DP (2001) Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl Environ Microbiol 67:4708–4716CrossRefGoogle Scholar
  159. Smyth GK, Speed T (2003) Normalization of cDNA microarray data. Methods 31:265–273CrossRefGoogle Scholar
  160. Sohail M, Akhtar S, Southern EM (1999) The folding of large RNAs studied by hybridization to arrays of complementary oligonucleotides. RNA 5:646–655CrossRefGoogle Scholar
  161. Southern EM (1989) Analysing polynucleotide sequences. 19891100 GB Ref Type: PatentGoogle Scholar
  162. Southern EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503–517CrossRefGoogle Scholar
  163. Southern EM, Case-Green SC, Elder JK, Johnson M, Mir KU, Wang L, Williams JC (1994) Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids. Nucleic Acids Res 22:1368–1373CrossRefGoogle Scholar
  164. Southern EM, Mir K, Shchepinov M (1999) Molecular interactions on microarrays. Nat Genet 21:5–9CrossRefGoogle Scholar
  165. Stenger DA, Andreadis JD, Vora GJ, Pancrazio JJ (2002) Potential applications of DNA microarrays in biodefense-related diagnostics. Curr Opin Biotechnol 13:208–212CrossRefGoogle Scholar
  166. Stimpson DI, Cooley PW, Knepper SM, Wallace DB (1998) Parallel production of oligonucleotide arrays using membranes and reagent jet printing. Biotechniques 25:886–890Google Scholar
  167. Stowe-Evans EL, Ford J, Kehoe DM (2004) Genomic DNA microarray analysis: identification of new genes regulated by light color in the cyanobacterium Fremyella diplosiphon. J Bacteriol 186:4338–4349Google Scholar
  168. Straub TM, Chandler DP (2003) Towards a unified system for detecting waterborne pathogens. J Microbiol Methods 53:185–197CrossRefGoogle Scholar
  169. Strezoska Z, Paunesku T, Radosavljevic D, Labat I, Drmanac R, Crkvenjakov R (1991) DNA sequencing by hybridization: bases read by a non-gel-based method. Proc Natl Acad Sci U S A 88:10089–10093CrossRefGoogle Scholar
  170. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A 96:2907–2912CrossRefGoogle Scholar
  171. Taroncher-Oldenburg G, Griner EM, Francis CA, Ward BB (2003) Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol 69:1159–1171CrossRefGoogle Scholar
  172. Taylor S, Smith S, Windle B, Guiseppi-Elie A (2003) Impact of surface chemistry and blocking strategies on DNA microarrays. Nucleic Acids Res 31:e87CrossRefGoogle Scholar
  173. Thiyagarajan S, Karhanek M, Akhras M, Davis RW, Pourmand N (2006) PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens. BMC Bioinformatics 7:500CrossRefGoogle Scholar
  174. Tiquia SM, Wu L, Chong SC, Passovets S, Xu D, Xu Y, Zhou J (2004) Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques 36:664–665Google Scholar
  175. Treimo J, Vegarud G, Langsrud T, Marki S, Rudi K (2006) Total bacterial and species-specific 16S rDNA micro-array quantification of complex samples. J Appl Microbiol 100:985–998CrossRefGoogle Scholar
  176. Troesch A, Nguyen H, Miyada CG, Desvarenne S, Gingeras TR, Kaplan PM, Cros P, Mabilat C (1999) Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays. J Clin Microbiol 37:49–55Google Scholar
  177. Tseng GC, Oh MK, Rohlin L, Liao JC, Wong WH (2001) Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res 29:2549–2557CrossRefGoogle Scholar
  178. Urakawa H, El Fantroussi S, Smidt H, Smoot JC, Tribou EH, Kelly JJ, Noble PA, Stahl DA (2003) Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Appl Environ Microbiol 69:2848–2856CrossRefGoogle Scholar
  179. Urakawa H, Noble PA, El Fantroussi S, Kelly JJ, Stahl DA (2002) Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses. Appl Environ Microbiol 68:235–244CrossRefGoogle Scholar
  180. Vainrub A, Pettitt BM (2002) Coulomb blockage of hybridization in two-dimensional DNA arrays. Phys Rev E Stat Nonlin Soft Matter Phys 66:041905Google Scholar
  181. van Bakel H, Holstege FC (2004) In control: systematic assessment of microarray performance. EMBO Rep 5:964–969CrossRefGoogle Scholar
  182. van Leeuwen WB, Jay C, Snijders S, Durin N, Lacroix B, Verbrugh HA, Enright MC, Troesch A, Van Belkum A (2003) Multilocus sequence typing of Staphylococcus aureus with DNA array technology. J Clin Microbiol 41:3323–3326CrossRefGoogle Scholar
  183. Volokhov D, Rasooly A, Chumakov K, Chizhikov V (2002) Identification of listeria species by microarray-based assay. J Clin Microbiol 40:4720–4728CrossRefGoogle Scholar
  184. Voordouw G, Voordouw JK, Karkhoff-Schweizer RR, Fedorak PM, Westlake DW (1991) Reverse sample genome probing, a new technique for identification of bacteria in environmental samples by DNA hybridization, and its application to the identification of sulfate-reducing bacteria in oil field samples. Appl Environ Microbiol 57:3070–3078Google Scholar
  185. Vora GJ, Meador CE, Stenger DA, Andreadis JD (2004) Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Appl Environ Microbiol 70:3047–3054CrossRefGoogle Scholar
  186. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL (2002) Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci U S A 99:15687–15692CrossRefGoogle Scholar
  187. Wang RF, Beggs ML, Erickson BD, Cerniglia CE (2004) DNA microarray analysis of predominant human intestinal bacteria in fecal samples. Mol Cell Probes 18:223–234CrossRefGoogle Scholar
  188. Wilson CL, Pepper SD, Hey Y, Miller CJ (2004) Amplification protocols introduce systematic but reproducible errors into gene expression studies. Biotechniques 36:498–506Google Scholar
  189. Wilson KH, Wilson WJ, Radosevich JL, DeSantis TZ, Viswanathan VS, Kuczmarski TA, Andersen GL (2002) High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol 68:2535–2541CrossRefGoogle Scholar
  190. Wong CW, Albert TJ, Vega VB, Norton JE, Cutler DJ, Richmond TA, Stanton LW, Liu ET, Miller LD (2004) Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays. Genome Res 14:398–405CrossRefGoogle Scholar
  191. Wu L, Thompson DK, Li G, Hurt RA, Tiedje JM, Zhou J (2001) Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol 67:5780–5790CrossRefGoogle Scholar
  192. Wu Y, de Kievit P, Vahlkamp L, Pijnenburg D, Smit M, Dankers M, Melchers D, Stax M, Boender PJ, Ingham C, Bastiaensen N, de Wijn R, van Alewijk D, van Damme H, Raap AK, Chan AB, van Beuningen R (2004) Quantitative assessment of a novel flow-through porous microarray for the rapid analysis of gene expression profiles. Nucleic Acids Res 32:e123CrossRefGoogle Scholar
  193. Xiang CC, Chen M, Ma L, Phan QN, Inman JM, Kozhich OA, Brownstein MJ (2003) A new strategy to amplify degraded RNA from small tissue samples for microarray studies. Nucleic Acids Res 31:e53CrossRefGoogle Scholar
  194. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30:e15CrossRefGoogle Scholar
  195. Yang YH, Speed T (2002) Design issues for cDNA microarray experiments. Nat Rev Genet 3:579–588Google Scholar
  196. Ye RW, Wang T, Bedzyk L, Croker KM (2001) Applications of DNA microarrays in microbial systems. J Microbiol Methods 47:257–272CrossRefGoogle Scholar
  197. Yershov G, Barsky V, Belgovskiy A, Kirillov E, Kreindlin E, Ivanov I, Parinov S, Guschin D, Drobishev A, Dubiley S, Mirzabekov A (1996) DNA analysis and diagnostics on oligonucleotide microchips. Proc Natl Acad Sci U S A 93:4913–4918CrossRefGoogle Scholar
  198. Yue H, Eastman PS, Wang BB, Minor J, Doctolero MH, Nuttall RL, Stack R, Becker JW, Montgomery JR, Vainer M, Johnston R (2001) An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nucleic Acids Res 29:E41CrossRefGoogle Scholar
  199. Zaigler A, Schuster SC, Soppa J (2003) Construction and usage of a onefold-coverage shotgun DNA microarray to characterize the metabolism of the archaeon Haloferax volcanii. Mol Microbiol 48:1089–1105CrossRefGoogle Scholar
  200. Zammatteo N, Jeanmart L, Hamels S, Courtois S, Louette P, Hevesi L, Remacle J (2000) Comparison between different strategies of covalent attachment of DNA to glass surfaces to build DNA microarrays. Anal Biochem 280:143–150CrossRefGoogle Scholar
  201. Zhang L, Hurek T, Reinhold-Hurek B (2006) A nifH-based oligonucleotide microarray for functional diagnostics of nitrogen-fixing microorganisms. Microb EcolGoogle Scholar
  202. Zhou J, Thompson DK (2002) Challenges in applying microarrays to environmental studies. Curr Opin Biotechnol 13:204–207CrossRefGoogle Scholar
  203. Zwick ME, Mcafee F, Cutler DJ, Read TD, Ravel J, Bowman GR, Galloway DR, Mateczun A (2005) Microarray-based resequencing of multiple Bacillus anthracis isolates. Genome Biol 6:R10CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Tanja Kostic
    • 1
  • Patrice Francois
    • 2
  • Levente Bodrossy
    • 1
  • Jacques Schrenzel
    • 3
  1. 1.Department of BioresourcesAustrian Research Centres GmbH - ARCAustria
  2. 2.Genomic Research Laboratory, Division of Infectious Diseases, University of Geneva Hospital Rue Micheli-du-crestSwitzerland
  3. 3.Hospital of Geneva Department of Internal MedicineGenomic Research Laboratory and Clinical Microbiology Laboratory Service of Infectious Diseases UniversityGenevaSwitzerland

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