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).