Advertisement

Analytical and Bioanalytical Chemistry

, Volume 406, Issue 14, pp 3323–3334 | Cite as

Oligonucleotide microarray chip for the quantification of MS2, ΦX174, and adenoviruses on the multiplex analysis platform MCR 3

  • Sandra Lengger
  • Johannes Otto
  • Dennis Elsässer
  • Oliver Schneider
  • Andreas Tiehm
  • Jens Fleischer
  • Reinhard Niessner
  • Michael SeidelEmail author
Research Paper
Part of the following topical collections:
  1. Multiplex Platforms in Diagnostics and Bioanalytics

Abstract

Pathogenic viruses are emerging contaminants in water which should be analyzed for water safety to preserve public health. A strategy was developed to quantify RNA and DNA viruses in parallel on chemiluminescence flow-through oligonucleotide microarrays. In order to show the proof of principle, bacteriophage MS2, ΦX174, and the human pathogenic adenovirus type 2 (hAdV2) were analyzed in spiked tap water samples on the analysis platform MCR 3. The chemiluminescence microarray imaging unit was equipped with a Peltier heater for a controlled heating of the flow cell. The efficiency and selectivity of DNA hybridization could be increased resulting in higher signal intensities and lower cross-reactivities of polymerase chain reaction (PCR) products from other viruses. The total analysis time for DNA/RNA extraction, cDNA synthesis for RNA viruses, polymerase chain reaction, single-strand separation, and oligonucleotide microarray analysis was performed in 4–4.5 h. The parallel quantification was possible in a concentration range of 9.6 × 105–1.4 × 1010 genomic units (GU)/mL for bacteriophage MS2, 1.4 × 105–3.7 × 108 GU/mL for bacteriophage ΦX174, and 6.5 × 103–1.2 × 105 for hAdV2, respectively, by using a measuring temperature of 40 °C. Detection limits could be calculated to 6.6 × 105 GU/mL for MS2, 5.3 × 103 GU/mL for ΦX174, and 1.5 × 102 GU/mL for hAdV2, respectively. Real samples of surface water and treated wastewater were tested. Generally, found concentrations of hAdV2, bacteriophage MS2, and ΦX174 were at the detection limit. Nevertheless, bacteriophages could be identified with similar results by means of quantitative PCR and oligonucleotide microarray analysis on the MCR 3.

Keywords

Fluorescence/luminescence Biochips/high-throughput screening Bioanalytical methods 

Notes

Acknowledgement

The authors like to thank the BMBF for financial support (project PATH2OGENSCAN, 02WU1142, 02WU1143, 02WU1144, 02WU1145) in the field of MCR 3 optimization. Especially we want to thank GWK Präzisionstechnik GmbH for their collaboration in the project and the supply of the MCR 3 research device for oligonucleotide microarray analysis. Also thanks to Huntsman Corporation (Rotterdam, the Netherlands) for the kindly provided free DAPEG samples.

Supplementary material

216_2014_7641_MOESM1_ESM.pdf (207 kb)
ESM 1 (PDF 206 kb)

References

  1. 1.
    Fong T, Lipp EK (2005) Microbiol Mol Biol Rev 69:357–371CrossRefGoogle Scholar
  2. 2.
    Bosch A (1998) Int Microbiol 1:191–196Google Scholar
  3. 3.
    Fout GS, Martinson BC, Moyer MWN, Dahling DR (2003) Appl Environ Microbiol 69:3158–3164CrossRefGoogle Scholar
  4. 4.
    Lee S, Kim S (2002) Water Res 36:248–256CrossRefGoogle Scholar
  5. 5.
    Lodder WJ, de Roda Husman AM (2005) Appl Environ Microbiol 71:1453–1461CrossRefGoogle Scholar
  6. 6.
    Hamza IA, Jurzik L, Überla K, Wilhelm M (2011) Int J Hyg Environ Health 214:424–436CrossRefGoogle Scholar
  7. 7.
    Keswick BH, Satterwhite TK, Johnson PC, DuPont HL, Secor SL, Bitsura JA, Gary GW, Hoff JC (1985) Appl Environ Microbiol 50:261–264Google Scholar
  8. 8.
    Gerba CP, Gramos DM, Nwachuku N (2002) Appl Environ Microbiol 68:5167–5169CrossRefGoogle Scholar
  9. 9.
    Connelly JT, Baeumner AJ (2012) Anal Bioanal Chem 402:117–127CrossRefGoogle Scholar
  10. 10.
    Haas CN, Rose JB, Gerba C, Regli S (1993) Risk Anal 13:545–552CrossRefGoogle Scholar
  11. 11.
    Heller MJ (2002) Annu Rev Biomed Eng 4:129–153CrossRefGoogle Scholar
  12. 12.
    Pappaert K, Van Hummelen P, Vanderhoeven J, Baron GV, Desmet G (2003) Chem Eng Sci 58:4921–4930CrossRefGoogle Scholar
  13. 13.
    Donhauser SC, Niessner R, Seidel M (2009) Anal Sci 25:669–674CrossRefGoogle Scholar
  14. 14.
    Seidel M, Niessner R (2008) Anal Bioanal Chem 391:1521–1544CrossRefGoogle Scholar
  15. 15.
    Lehr HP, Reimann M, Brandenburg A, Sulz G, Klapproth H (2003) Anal Chem 75:2414–2420CrossRefGoogle Scholar
  16. 16.
    Brandstetter T, Böhmer S, Prucker O, Bissé E, zur Hausen A, Alt-Mörbe J, Rühe J (2009) J Virol Methods 163:40–48CrossRefGoogle Scholar
  17. 17.
    Tran PH, Peiffer DA, Shin Y, Meek LM, Brody JP, Cho KWY (2002) Nucleic Acids Res 30:e54CrossRefGoogle Scholar
  18. 18.
    Albers J, Grunwald T, Nebling E, Piechotta G, Hintsche R (2003) Anal Bioanal Chem 377:521–527CrossRefGoogle Scholar
  19. 19.
    Elsholz B, Nitsche A, Achenbach J, Ellerbrok H, Blohm L, Albers J, Pauli G, Hintsche R, Wörl R (2009) Biosens Bioelectron 24:1737–1743CrossRefGoogle Scholar
  20. 20.
    Roda A, Guardigli M, Michelini E, Mirasoli M, Pasini P (2003) Anal Chem 75:462–470CrossRefGoogle Scholar
  21. 21.
    Kloth K, Niessner R, Seidel M (2009) Biosens Bioelectron 24:2106–2112CrossRefGoogle Scholar
  22. 22.
    Kloth K, Rye-Johnsen M, Didier A, Dietrich R, Märtlbauer E, Niessner R, Seidel M (2009) Analyst 134:1433–1439CrossRefGoogle Scholar
  23. 23.
    Wutz K, Niessner R, Seidel M (2011) Microchim Acta 173:1–9CrossRefGoogle Scholar
  24. 24.
    Szkola A, Campbell K, Elliott CP, Niessner R, Seidel M (2013) Anal Chim Acta 797:211–218CrossRefGoogle Scholar
  25. 25.
    Huebner M, Wutz K, Szkola A, Niessner R, Seidel M (2013) Anal Sci 29:461–466CrossRefGoogle Scholar
  26. 26.
    Wutz K, Meyer VK, Wachek S, Krol P, Gareis M, Nölting C, Struck F, Soutschek E, Böcher O, Niessner R, Seidel M (2013) Anal Chem 85:5279–5285CrossRefGoogle Scholar
  27. 27.
    Donhauser SC, Niessner R, Seidel M (2011) Anal Chem 83:3153–3160CrossRefGoogle Scholar
  28. 28.
    Fish DJ, Horne MT, Brewood JP, Goodarzi JP, Alemayehu S, Bhandiwad A, Searles RP, Benight AS (2007) Nucleic Acids Res 35:7197–7208CrossRefGoogle Scholar
  29. 29.
    Bodrossy L, Sessitsch A (2004) Curr Opin Microbiol 7:245–254CrossRefGoogle Scholar
  30. 30.
    Feng J, Wang Y, Cao G, Hu S, Kuang X, Tang S, You S, Liu L (2013) Eur Food Res 236:1073–1083CrossRefGoogle Scholar
  31. 31.
    Ballarani A, Segata N, Huttenhower C, Jousson O (2013) PLoS ONE 8:e55764CrossRefGoogle Scholar
  32. 32.
    Wolter A, Niessner R, Seidel M (2007) Anal Chem 79:4529–4537CrossRefGoogle Scholar
  33. 33.
    Dreier J, Störmer M, Kleesiek K (2005) J Clin Microbiol 43:4551–4557CrossRefGoogle Scholar
  34. 34.
    Crews N, Wittwer C, Gale B (2008) Biomed Microdevices 10:187–195CrossRefGoogle Scholar
  35. 35.
    Heim A, Ebnet C, Harste G, Pring-Ǻkerblom P (2003) J Med Virol 70:228–239CrossRefGoogle Scholar
  36. 36.
    Katayama H, Shimasaki A, Ohgaki S (2002) Appl Environ Microbiol 68:1033–1039CrossRefGoogle Scholar
  37. 37.
    Vilaginès P, Sarrette B, Husson G, Vilaginès R (1993) Water Sci Technol 27:299–306CrossRefGoogle Scholar
  38. 38.
    Saiyed ZM, Telang SD, Ramchand CN (2003) Biomagn Res Technol 1:2CrossRefGoogle Scholar
  39. 39.
    Markham NR, Zuker M (2005) Nucleic Acids Res 33:577–581CrossRefGoogle Scholar
  40. 40.
    Markham NR, Zuker M (2008) In: Keith JM (ed) Bioinformatics, Volume II. Structure, function and applications. Humana, Totowa, pp 3–31Google Scholar
  41. 41.
    Johnstone RW, Andrew AM, Hogarth MP, Pietersz G, McKenzie IFC (1990) Mol Immunol 27:327–333CrossRefGoogle Scholar
  42. 42.
    Vermeer AWP, Bremer MGEG, Norde W (1998) Biochim Biophys Acta Gen Subj 1425:1–12CrossRefGoogle Scholar
  43. 43.
    Chattopadhyay K, Mazumdar M (2000) Biochemistry 39:263–270CrossRefGoogle Scholar
  44. 44.
    Cansiz S, Özen C, Bayrac C, Bayrac AT, Gül F, Kavruk M, Yilmaz R, Eyidogan F, Öktem HY (2012) Eur Food Res Technol 235:429–437CrossRefGoogle Scholar
  45. 45.
    Kuo DHW, Simmons FJ, Blair S, Hart E, Rose JB, Xagoraraki I (2010) Water Res 44:1520–1530CrossRefGoogle Scholar
  46. 46.
    Fong TT, Phanikumar MS, Xagoraraki I, Rose JB (2009) Appl Environ Microbiol 76:715–723CrossRefGoogle Scholar
  47. 47.
    Ikner LA, Gerba CP, Bright KR (2012) Food Environ Virol 4:41–67CrossRefGoogle Scholar
  48. 48.
    Abbaszadegan M, Huber MS, Gerba CP, Pepper IL (1993) Appl Environ Microbiol 59:1318–1324Google Scholar
  49. 49.
    Pei L, Rieger M, Lengger S, Ott S, Zawadsky C, Hartmann NM, Selinka HC, Tiehm A, Niessner R, Seidel M (2012) Environ Sci Technol 46:10073–10080Google Scholar
  50. 50.
    Lengger S, Niessner R, Seidel M (2012) Nachr Chemie 60:1208–1212CrossRefGoogle Scholar
  51. 51.
    WHO (2011) Guidelines for drinking water quality, 4th edn. World Health Organization, GenevaGoogle Scholar
  52. 52.
    Grabow WOK (2001) Water SA 28:251–266Google Scholar
  53. 53.
    Kundu A, McBride G, Wuertz S (2013) Water Res 47:6309–6325CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Sandra Lengger
    • 1
  • Johannes Otto
    • 2
  • Dennis Elsässer
    • 1
  • Oliver Schneider
    • 3
  • Andreas Tiehm
    • 2
  • Jens Fleischer
    • 3
  • Reinhard Niessner
    • 1
  • Michael Seidel
    • 1
    Email author
  1. 1.Chair for Analytical Chemistry and Institute of HydrochemistryTechnische Universität MünchenMunichGermany
  2. 2.Department of Environmental BiotechnologyDVGW-Technologiezentrum WasserKarlsruheGermany
  3. 3.District Government Stuttgart, State Health AgencyLandesgesundheitsamt Baden-WürttembergStuttgartGermany

Personalised recommendations