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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.
A universal method enables high-specificity, unbiased pathogen detection from diverse body fluids using metagenomic sequencing and may accelerate clinical decisions.
Details
; Sample, Hannah 3 ; Yu Guixia 1 ; Ishpuniani Gurpreet 1 ; Briggs, Benjamin 1 ; Chow, Eric D 3
; Berger, Amy 4 ; Wilson, Michael R 5
; Wang, Candace 1 ; Hsu, Elaine 6 ; Miller, Steve 1 ; DeRisi, Joseph L 7 ; Chiu, Charles Y 8
1 University of California San Francisco, Department of Laboratory Medicine, San Francisco, USA (GRID:grid.266102.1) (ISNI:0000 0001 2297 6811); UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, USA (GRID:grid.266102.1) (ISNI:0000 0001 2297 6811)
2 Leeds Teaching Hospitals NHS Trust, Leeds, UK (GRID:grid.415967.8) (ISNI:0000 0000 9965 1030)
3 University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, USA (GRID:grid.266102.1) (ISNI:0000 0001 2297 6811)
4 University of California San Francisco, Department of Medicine, San Francisco, USA (GRID:grid.266102.1) (ISNI:0000 0001 2297 6811)
5 University of California San Francisco, Weill Institute for Neurosciences, San Francisco, USA (GRID:grid.266102.1) (ISNI:0000 0001 2297 6811); University of California San Francisco, Department of Neurology, San Francisco, USA (GRID:grid.266102.1) (ISNI:0000 0001 2297 6811)
6 University of California San Francisco, Department of Laboratory Medicine, San Francisco, USA (GRID:grid.266102.1) (ISNI:0000 0001 2297 6811)
7 University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, USA (GRID:grid.266102.1) (ISNI:0000 0001 2297 6811); Chan Zuckerberg Biohub, San Francisco, USA (GRID:grid.499295.a)
8 University of California San Francisco, Department of Laboratory Medicine, San Francisco, USA (GRID:grid.266102.1) (ISNI:0000 0001 2297 6811); UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, USA (GRID:grid.266102.1) (ISNI:0000 0001 2297 6811); University of California San Francisco, Department of Medicine, Division of Infectious Diseases, San Francisco, USA (GRID:grid.266102.1) (ISNI:0000 0001 2297 6811)