Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids

Nat Med. 2021 Jan;27(1):115-124. doi: 10.1038/s41591-020-1105-z. Epub 2020 Nov 9.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • Body Fluids / microbiology*
  • Cell-Free Nucleic Acids / analysis
  • Cell-Free Nucleic Acids / genetics
  • Female
  • Fungi / genetics
  • Fungi / isolation & purification*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Male
  • Metagenomics*
  • Middle Aged


  • Cell-Free Nucleic Acids