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Comparison of isothermal helicase-dependent amplification and PCR for the detection of Mycobacterium tuberculosis by an electrochemical genomagnetic assay

Analytical and Bioanalytical Chemistry volume 408, pages 8603–8610 (2016)Cite this article

Abstract

Methods for the early and sensitive detection of pathogenic bacteria suited to low-resource settings could impact diagnosis and management of diseases. Helicase-dependent isothermal amplification (HDA) is an ideal tool for this purpose, especially when combined with a sequence-specific detection method able to improve the selectivity of the assay. The implementation of this approach requires that its analytical performance is shown to be comparable with the gold standard method, polymerase chain reaction (PCR). In this study, we optimize and compare the asymmetric amplification of an 84-base-long DNA sequence specific for Mycobacterium tuberculosis by PCR and HDA, using an electrochemical genomagnetic assay for hybridization-based detection of the obtained single-stranded amplicons. The results indicate the generalizability of the magnetic platform with electrochemical detection for quantifying amplification products without previous purification. Moreover, we demonstrate that under optimal conditions the same gene can be amplified by either PCR or HDA, allowing the detection of as low as 30 copies of the target gene sequence with acceptable reproducibility. Both assays have been applied to the detection of M. tuberculosis in sputum, urine, and pleural fluid samples with comparable results. Simplicity and isothermal nature of HDA offer great potential for the development of point-of-care devices.

Comparative evaluation of isothermal helicase-dependent amplification and PCR for electrochemical detection of Mycobacterium tuberculosis

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Acknowledgments

This research has been supported by the Spanish Ministerio de Economía y Competitividad (project CTQ2012-31157), the European Regional Development Fund, and Principado de Asturias government (FC-15-GRUPIN14-025). RMC thanks Principado de Asturias government and FICYT for a Clarín post-doctoral contract. We thank Dr. Juan José Palacios-Gutiérrez from Hospital Universitario de Asturias for providing the clinical samples.

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Authors and Affiliations

  1. Dpto. Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006, Oviedo, Spain

    Susana Barreda-García, Rebeca Miranda-Castro, Noemí de-los-Santos-Álvarez, Arturo J. Miranda-Ordieres & M. Jesús Lobo-Castañón

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  1. Susana Barreda-García
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  2. Rebeca Miranda-Castro
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  3. Noemí de-los-Santos-Álvarez
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  4. Arturo J. Miranda-Ordieres
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  5. M. Jesús Lobo-Castañón
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Correspondence to M. Jesús Lobo-Castañón.

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Published in the topical collection Isothermal Nucleic Acid Amplification in Bioanalysis with guest editor Maria Jesus Lobo Castañón.

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Barreda-García, S., Miranda-Castro, R., de-los-Santos-Álvarez, N. et al. Comparison of isothermal helicase-dependent amplification and PCR for the detection of Mycobacterium tuberculosis by an electrochemical genomagnetic assay. Anal Bioanal Chem 408, 8603–8610 (2016). https://doi.org/10.1007/s00216-016-9514-z

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  • DOI: https://doi.org/10.1007/s00216-016-9514-z

Keywords

  • Genomagnetic assay
  • Helicase
  • Isothermal amplification
  • PCR
  • Mycobacterium tuberculosis