Abstract

The emergence of pathogens resistant to existing antimicrobial drugs is a growing worldwide health crisis that threatens a return to the pre-antibiotic era. To decrease the overuse of antibiotics, molecular diagnostics systems are needed that can rapidly identify pathogens in a clinical sample and determine the presence of mutations that confer drug resistance at the point of care. We developed a fully integrated, miniaturized semiconductor biochip and closed-tube detection chemistry that performs multiplex nucleic acid amplification and sequence analysis. The approach had a high dynamic range of quantification of microbial load and was able to perform comprehensive mutation analysis on up to 1,000 sequences or strands simultaneously in <2 h. We detected and quantified multiple DNA and RNA respiratory viruses in clinical samples with complete concordance to a commercially available test. We also identified 54 drug-resistance-associated mutations that were present in six genes of Mycobacterium tuberculosis, all of which were confirmed by next-generation sequencing.

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Acknowledgements

The authors thank J. SantaLucia and the staff of DNA Software for their technical support and suggestions related to thermodynamic simulations for primer and probe design. Research reported in this publication was supported by the National Human Genome Research Institute of the National Institutes of Health under award R44HG007626. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

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Affiliations

  1. InSilixa, Inc., Sunnyvale, California, USA.

    • Arjang Hassibi
    • , Arun Manickam
    • , Rituraj Singh
    • , Sara Bolouki
    • , Ruma Sinha
    • , Kshama B Jirage
    • , Mark W McDermott
    • , Gelareh Mazarei
    • , Lei Pei
    • , Luc Bousse
    • , Mark Miller
    • , Mehrdad Heshami
    • , Michael P Savage
    • , Michael T Taylor
    • , Nader Gamini
    • , Nicholas Wood
    • , Pallavi Mantina
    • , Patrick Grogan
    • , Peter Kuimelis
    • , Piyush Savalia
    • , Scott Conradson
    • , Yuan Li
    • , Rich B Meyer
    • , Edmond Ku
    • , Jessica Ebert
    • , Gregory Dolganov
    • , Tran Van
    • , Kirsten A Johnson
    • , Pejman Naraghi-Arani
    • , Robert G Kuimelis
    •  & Gary Schoolnik
  2. Electrical Engineering Department, California Institute of Technology, Pasadena, California, USA.

    • Babak Hassibi
  3. Electrical and Computer Engineering Department, University of Texas at Austin, Austin, Texas, USA.

    • Haris Vikalo
  4. Department of Medicine, Stanford University, Stanford, California, USA.

    • Benjamin A Pinsky
    •  & Gary Schoolnik

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Contributions

A.H. conceived the technology. A.H., R.G.K. and G.S. co-supervised the project and wrote the manuscript with input from the other authors. Integrated biochip and optoelectronic components were designed and built by A.M., R. Singh, M.W.M., M.M., M.H., N.W. and E.K. In silico assay design and signal processing algorithms were developed by S.B., J.E., R. Sinha, P.K., B.H. and H.V. Assay implementation and performance validation on clinical samples were executed by P.N., G.D., K.A.J., T.V., G.M., K.B.J., L.P., M.P.S., P.M., B.A.P. and Y.L. Key technical contributions for chemistry, mechanical design and fluidics were provided by P.G., L.B., P.S., N.G., M.T.T., R.B.M. and S.C.

Competing interests

All of the authors listed in this paper were employees or contractors of InSilixa, Inc., with the exception of B.H., H.V. and B.A.P., who were academic collaborators on the project.

Corresponding author

Correspondence to Arjang Hassibi.

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DOI

https://doi.org/10.1038/nbt.4179