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Metagenomic Nanopore Sequencing for Precision Diagnosis of Infectious Diseases


Metagenomic next-generation sequencing (mNGS) holds great promise for infectious disease diagnosis because of capacity to identify all potential pathogens – bacteria, viruses, fungi, and parasites – in a single assay. In June 2017, we completed the PDAID (“Precision Diagnosis of Acute Infectious Diseases”) study, a multi-hospital, nationwide prospective study of 220 patients, to evaluate the utility, outcome impact, and cost-effectiveness of a CLIA (Clinical Laboratory Improvement Amendments)-validated mNGS Illumina-based assay versus conventional microbiological testing for diagnosis of infectious causes of meningitis and encephalitis. We will discuss interim results from the PDAID study, and extension of mNGS to real-time metagenomic diagnosis of febrile illnesses in the field on a nanopore platform (the MinION sequencer from Oxford Nanopore Technologies). We will also discuss recent technological improvements that enable rapid and high-sensitivity detection (102 copies/mL) of pathogens from clinical body fluid samples, including the implementation of a “spiked primer” approach and the development of the SURPIrt real-time computational platform, which can analyze up to 1 million reads in <10 minutes on a laptop. Finally, we will describe ongoing efforts to clinically validate the nanopore platform in a CLIA laboratory, and to deploy this platform in remote field settings for infectious diseases testing, ranging from pandemic “hotspots” in Africa to outer space aboard the International Space Station (ISS).

Authors: Charles Chiu

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