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

Hassibi, Arjang; Manickam, Arun; Singh, Rituraj; Bolouki, Sara; Sinha, Ruma; Jirage, Kshama B; McDermott, Mark W; Hassibi, Babak; Vikalo, Haris; Mazarei, Gelareh; Pei, Lei; Bousse, Luc; Miller, Mark; Heshami, Mehrdad; Savage, Michael P; Taylor, Michael T; Gamini, Nader; Wood, Nicholas; Mantina, Pallavi; Grogan, Patrick

Rapid, multiplex identification of pathogens and disease-associated mutations is possible with a new 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.

Nature Biotechnology, 2022, Vol 40, Issue 8, p738

1087-0156

Academic Journal

10.1038/nbt.4179