Multiplexed identification, quantification and genotyping of infectious agents using a semiconductor biochip

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. ; © 2018 Springer Nature Limited. Received 16 March 2017; accepted 23 May 2018; published online 16 July 2018. 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. Author 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., ...