| Literature DB >> 33169017 |
Wei Gu1,2, Xianding Deng1,2, Marco Lee3, Yasemin D Sucu1,2, Shaun Arevalo1,2, Doug Stryke1,2, Scot Federman1,2, Allan Gopez1,2, Kevin Reyes1,2, Kelsey Zorn4, Hannah Sample4, Guixia Yu1,2, Gurpreet Ishpuniani1,2, Benjamin Briggs1,2, Eric D Chow4, Amy Berger5, Michael R Wilson6,7, Candace Wang1,2, Elaine Hsu1, Steve Miller1,2, Joseph L DeRisi4,8, Charles Y Chiu9,10,11.
Abstract
We developed a metagenomic next-generation sequencing (mNGS) test using cell-free DNA from body fluids to identify pathogens. The performance of mNGS testing of 182 body fluids from 160 patients with acute illness was evaluated using two sequencing platforms in comparison to microbiological testing using culture, 16S bacterial PCR and/or 28S-internal transcribed ribosomal gene spacer (28S-ITS) fungal PCR. Test sensitivity and specificity of detection were 79 and 91% for bacteria and 91 and 89% for fungi, respectively, by Illumina sequencing; and 75 and 81% for bacteria and 91 and 100% for fungi, respectively, by nanopore sequencing. In a case series of 12 patients with culture/PCR-negative body fluids but for whom an infectious diagnosis was ultimately established, seven (58%) were mNGS positive. Real-time computational analysis enabled pathogen identification by nanopore sequencing in a median 50-min sequencing and 6-h sample-to-answer time. Rapid mNGS testing is a promising tool for diagnosis of unknown infections from body fluids.Entities:
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Year: 2020 PMID： 33169017 PMCID： PMC9020267 DOI： 10.1038/s41591-020-1105-z
Source DB: PubMed Journal: Nat Med ISSN： 1078-8956 Impact factor: 87.241