Biomedical Microdevices

, Volume 15, Issue 5, pp 821–830 | Cite as

On-chip parallel detection of foodborne pathogens using loop-mediated isothermal amplification

  • Carlos Duarte
  • Eric Salm
  • Brian Dorvel
  • Bobby ReddyJr.
  • Rashid Bashir


According to estimates issued by the Center for Disease Control and Prevention, one out of six Americans will get sick during this year due to consumption of contaminated products and there will be 50,000 related hospitalizations. To control and treat the responsible foodborne diseases, rapid and accurate detection of pathogens is extremely important. A portable device capable of performing nucleic acid amplification will enable the effective detection of infectious agents in multiple settings, leading to better enforcement of food safety regulations. This work demonstrates the multiplexed detection of food pathogens through loop-mediated isothermal amplification on a silicon chip. Silane passivation is used to prevent the adsorption of the polymerase on silicon oxide, which can severely inhibit nucleic acid amplification. We demonstrate the multiplexed screening of virulence genes of Listeria monocytogenes, Escherichia coli, and Salmonella by dehydrating the corresponding primers in oxidized silicon wells. Droplets of 30 nL with reagents for nucleic acid amplification and lysate of suspected pathogens are arrayed on micro-machined wells with an automated microinjection system. We show that dehydrated primers re-suspend when other reagents are microinjected, and the resulting mix can be used to specifically amplify the targeted gene. Results of characterization experiments demonstrate sensitivity down to a few templates per reaction, specificity that enables multiplexed screening, and robustness that allows amplification without DNA extraction.


Miniaturized DNA amplification Loop-mediated isothermal amplification Primer dehydration Silane passivation Multiplexed screening 

Supplementary material

10544_2013_9769_MOESM1_ESM.mpg (40.2 mb)
Supplementary Video 1Automated filling of micro array wells with microinjector. A silanized chip with dehydrated primers is covered in mineral oil for encapsulation. The microinjector systems automatically fills each well with around 30 nL of a primer-less LAMP solution with the target template. Including alignment steps, the full 6 × 6 array is filled in a total of about 3 min. After all wells are filled, the chip is heated to 65 °C for amplification. (MPG 41200 kb)


  1. T. Abe, Y. Segawa, H. Watanabe, T. Yotoriyama, S. Kai, A. Yasuda, N. Shimizu, N. Tojo, Lab Chip 11, 6 (2011)CrossRefGoogle Scholar
  2. F. Ahmad, S.A. Hashsham, Anal. Chim. Acta 733, 1–15 (2012)CrossRefGoogle Scholar
  3. F. Ahmad, G. Seyrig, D.M. Tourlousse, R.D. Stedtfeld, J.M. Tiedje, S.A. Hashsham, Biomed. Microdevices 13, 5 (2011)CrossRefGoogle Scholar
  4. T.J. Anchordoquy, M.C. Molina, Cell Preserv. Technol. 5, 4 (2007)CrossRefGoogle Scholar
  5. Centers for Disease Control and Prevention, CDC estimates of foodborne illness in the United States. Accessed 21 March 2013.
  6. S. Chen, F. Wang, J.C. Beaulieu, R.E. Stein, B. Ge, Appl. Environ. Microbiol. 77, 12 (2011)Google Scholar
  7. P. Craw, W. Balachandran, Lab Chip 12, 14 (2012)CrossRefGoogle Scholar
  8. J. Hedman, P. Radstrom, PCR Detection of Microbial Pathogens, 2nd edn. (Humana Press, Totowa, 2012), pp. 17–48Google Scholar
  9. C. Holland, F.L. Kiechle, Curr. Opin. Microbiol. 8, 5 (2005)CrossRefGoogle Scholar
  10. N. Jokilaakso, E. Salm, A. Chen, L. Millet, C. Duarte-Guevara, B. Dorvel, B. Reddy, A.E. Karlstrom, Y. Chen, H. Ji, R. Sooryakumar, R. Bashir, Lab Chip 13, 3 (2013)CrossRefGoogle Scholar
  11. Y. Kimura, M.J.L. de Hoon, S. Aoki, Y. Ishizu, Y. Kawai, Y. Kogo, C.O. Daub, A. Lezhava, E. Arner, Y. Hayashizaki, Nucleic Acids Res. 39, 9 (2011)CrossRefGoogle Scholar
  12. M.D.C. Molina, T.K. Armstrong, Y. Zhang, M.M. Patel, Y.K. Lentz, T.J. Anchordoquy, J. Pharm. Sci. 93, 9 (2004)CrossRefGoogle Scholar
  13. K. Nagamine, T. Hase, T. Notomi, Mol. Cell. Probes 16, 3 (2002)CrossRefGoogle Scholar
  14. New England Biolabs Inc., Bst 2.0 WarmStart DNA polymerase. Accessed 21 March 2013.
  15. S.K. Njoroge, H. Chen, M.A. Witek, S.A. Soper, Top Curr. Chem. 304 (2011).Google Scholar
  16. T. Notomi, H. Okayama, H. Masubuchi, T. Yonekawa, K. Watanabe, N. Amino, T. Hase, Nucleic Acids Res. 28, 12 (2000)CrossRefGoogle Scholar
  17. S. Park, Y. Zhang, S. Lin, T.-H. Wang, S. Yang, Biotechnol. Adv. 29, 6 (2011)CrossRefGoogle Scholar
  18. S. Purushothaman, C. Toumazou, C.-P. Ou, Sensors Actuators B Chem. 114, 2 (2006)CrossRefGoogle Scholar
  19. J.M. Rothberg, W. Hinz, T.M. Rearick, J. Schultz, W. Mileski, M. Davey et al., Nature 475, 7356 (2011)CrossRefGoogle Scholar
  20. E. Salm, C. Duarte-Guevara, P. Dak, B.R. Dorvel, B. Reddy, M.A. Alam, R. Bashir, PNAS 110, 9 (2013)CrossRefGoogle Scholar
  21. D.R. Seiner, H.A. Colburn, C. Baird, R.A. Bartholomew, T. Straub, K. Victry, J.R. Hutchison, N. Valentine, C.J. Bruckner-Lea, J. Appl. Microbiol. 114, 4 (2012)Google Scholar
  22. R.D. Stedtfeld, D.M. Tourlousse, G. Seyrig, T.M. Stedtfeld, M. Kronlein, S. Price, F. Ahmad, E. Gulari, J.M. Tiedje, S.A. Hashsham, Lab Chip 12, 8 (2012)CrossRefGoogle Scholar
  23. M.J. Tang, S. Zhou, X.-Y. Zhang, J.-H. Pu, Q.-L. Ge, X.-J. Tang, Y.-S. Gao, Curr. Microbiol. 63, 6 (2011)CrossRefGoogle Scholar
  24. W.E. Tenhaeff, K.K. Gleason, Adv. Funct. Mater. 18, 7 (2008)CrossRefGoogle Scholar
  25. D.M. Tourlousse, F. Ahmad, R.D. Stedtfeld, G. Seyrig, J.M. Tiedje, S. Hashsham, Biomed. Microdevices 14, 4 (2012)CrossRefGoogle Scholar
  26. U.S. Department of Agriculture Food Safety and Inspection Service (USDA-FSIS), Accredited laboratory program. Accessed 21 March 2013.
  27. W. Wang, H.-B. Wang, Z.-X. Li, Z.-Y. Guo, J. Biomed. Mater. Res. A 77, 1 (2006)Google Scholar
  28. F. Wang, L. Jiang, B. Ge, J. Clin. Microbiol. 50, 1 (2011)Google Scholar
  29. H. Wang, L. Wang, L. Yuan, W. Yang, J.L. Brash, H. Chen, Nanotechnology 23, 36 (2012)Google Scholar
  30. W. Wong, P. Georgiou, C.-P. Ou, C. Toumazou, Electron. Lett. 46, 5 (2010)CrossRefGoogle Scholar
  31. C. Zhang, D. Xing, Chem. Rev. 110, 8 (2010)CrossRefGoogle Scholar
  32. E. Zubritsky, Anal. Chem. 72, 23 (2000)Google Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Carlos Duarte
    • 1
    • 4
  • Eric Salm
    • 2
    • 4
  • Brian Dorvel
    • 3
    • 4
  • Bobby ReddyJr.
    • 1
    • 4
  • Rashid Bashir
    • 1
    • 2
    • 4
  1. 1.Department of Electrical and Computer Engineering, William L. Everitt LaboratoryUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  2. 2.Department of Bioengineering, 1270 Digital Computer LaboratoryUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  3. 3.Department of BiophysicsUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  4. 4.Micro and Nanotechnology LabUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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