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Integrating programmable DNAzymes with electrical readout for rapid and culture-free bacterial detection using a handheld platform

Nature Chemistry volume 13, pages 895–901 (2021)Cite this article

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Abstract

The detection and identification of bacteria currently rely on enrichment steps such as bacterial culture and nucleic acid amplification to increase the concentration of target analytes. These steps increase assay time, cost and complexity, making it difficult to realize a truly rapid point-of-care test. Here we report the development of an electrical assay that uses electroactive RNA-cleaving DNAzymes (e-RCDs) to identify specific bacterial targets and subsequently release a DNA barcode for transducing a signal onto an electrical chip. Integrating e-RCDs into a two-channel electrical chip with nanostructured electrodes provides the analytical sensitivity and specificity needed for clinical analysis. The e-RCD assay is capable of detecting 10 CFU (equivalent to 1,000 CFU ml–1) of Escherichia coli selectively from a panel containing multiple non-specific bacterial species. Clinical evaluation of this assay using 41 patient urine samples demonstrated a diagnostic sensitivity of 100% and specificity of 78% at an analysis time of less than one hour compared with the several hours needed for currently used culture-based methods.

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Fig. 1: Engineering the e-RCD assay.
Fig. 2: Bacterial detection using the e-RCD assay.
Fig. 3: Evaluation of the specificity of the e-RCD assay.
Fig. 4: Preclinical evaluation of the e-RCD assay for the detection of E. coli in urine.
Fig. 5: Demonstration of a point-of-care platform for E. coli detection in unprocessed urine.

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All relevant data presented in this study are provided in the article and its Supplementary Information. Source data are provided with this paper.

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Acknowledgements

We acknowledge J. Yang for her support in SEM imaging of nanostructured gold electrodes. We thank M. Gaskin for his support towards preparing and characterizing the clinical urine samples used in this study. We acknowledge the kind help of J. Gu with the ROC plot. We thank Y. Lu for helpful discussions. The work is supported by the Natural Science and Engineering Research Council (NSERC) of Canada. L.S. and T.H. are supported by the Canada Research Chair programme. The electron microscopy was carried out at the Canadian Centre for Electron Microscopy (CCEM), a national facility supported by the NSERC and McMaster University.

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Authors and Affiliations

  1. Department of Engineering Physics, McMaster University, Hamilton, Canada

    Richa Pandey & Leyla Soleymani

  2. Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada

    Dingran Chang & Yingfu Li

  3. Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada

    Marek Smieja

  4. Michael G. DeGroote Institute for Infectious Disease Research (IIDR), McMaster University, Hamilton, Canada

    Marek Smieja & Yingfu Li

  5. Department of Chemical Engineering, McMaster University, Hamilton, Canada

    Todd Hoare

  6. School of Biomedical Engineering, McMaster University, Hamilton, Canada

    Todd Hoare, Yingfu Li & Leyla Soleymani

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  1. Richa Pandey
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Contributions

R.P. designed and performed electrochemical experiments and co-wrote the manuscript. D.C. designed and performed molecular experiments and edited the manuscript. M.S. supervised and helped in designing the preclinical study. T.H. supervised the assay’s performance in biological samples and edited the manuscript. Y.L. supervised the overall assay and experimental design and edited the manuscript. L.S. contributed to the overall project design and supervision and co-wrote the manuscript. All authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to Yingfu Li or Leyla Soleymani.

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The authors declare no competing interests.

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Peer review information Nature Chemistry thanks Alexis Vallée-Bélisle and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Notes 1–9, Figs. 1–11, and Tables 1 and 2.

Source data

Source Data Fig. 1

Kinetics study data.

Source Data Fig. 2

Calibration plot data.

Source Data Fig. 3

Specificity data.

Source Data Fig. 4

Clinical testing data.

Source Data Fig. 5

Clinical testing data using chip-based pretreatment.

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Pandey, R., Chang, D., Smieja, M. et al. Integrating programmable DNAzymes with electrical readout for rapid and culture-free bacterial detection using a handheld platform. Nat. Chem. 13, 895–901 (2021). https://doi.org/10.1038/s41557-021-00718-x

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  • DOI: https://doi.org/10.1038/s41557-021-00718-x

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