Evidence map›Paper›PMID 33169017›Full record

ArticleNature medicine2021

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

Wei Gu, Xianding Deng, Marco Lee, Yasemin D Sucu, Shaun Arevalo, Doug Stryke, Scot Federman, Allan Gopez, Kevin Reyes, Kelsey Zorn and 12 more

Registry-linked trialOpen access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT04864873 (An External Evaluation of a Metagenomic Next Generation Sequencing Workflow for Infection Diagnosis Using Oxford Nanopore Sequencing.), which is not on this map. Cited by 428 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
428citing papers in PubMed, 2 pooled it
49.1field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

NCT04864873 naunknown statusnot on this map

An External Evaluation of a Metagenomic Next Generation Sequencing Workflow for Infection Diagnosis Using Oxford Nanopore Sequencing.

TypeinterventionalSponsorCapital and Coast District Health boardRan2021 to 2022Enrolled400ConditionsBacterial InfectionsArmsMetagenomic next generation sequencing using Oxford Nanopore, Standard microbiological diagnostic pathway
3 · Its place in the literature

Who cites it

428 citing papers in PubMed, 2 syntheses or guidelines pooled it, 661 citations in OpenAlex.

  1. Nanopore sequencing for microbiological diagnosis of bacterial pneumonia: A systematic review and meta-analysis.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026
    Pooled it
  2. Pooled it
  3. Trial
  4. Nanopore Sequencing for Chikungunya Virus: Principles and Application.Methods in molecular biology (Clifton, N.J.) · 2027
    Article
  5. Article
  6. Review
  7. Review
  8. Review
  9. Observational
  10. Review
  11. Clinical utility of metagenomic next-generation sequencing in precision diagnosis of infectious diseases: a retrospective study based on bronchoalveolar lavage fluid, blood, and cerebrospinal fluid.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026
    Article
  12. Article
  13. Metagenomic next-generation sequencing for comprehensive pathogen detection in intraocular infection.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026
    Article
  14. Article
  15. Article
  16. Review
  17. Review
  18. Article
  19. Article
  20. Development and genomic characterization of a diverse HIV-1 variant reference panel for nucleic acid-based testing.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2026
    Article

368 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

22 authors at 2 institutions in 2 countries.

Wei Gu *Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Xianding Deng *Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Marco Lee *Leeds Teaching Hospitals NHS Trust, Leeds, UK.
Yasemin D SucuDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Shaun ArevaloDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Doug StrykeDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Scot FedermanDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Allan GopezDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Kevin ReyesDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Kelsey ZornDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0003-1227-2137
Hannah SampleDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
Guixia YuDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Gurpreet IshpunianiDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Benjamin BriggsDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Eric D ChowDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-8079-918X
Amy BergerDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Michael R WilsonWeill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-8705-5084
Candace WangDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Elaine HsuDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Steve MillerDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Joseph L DeRisiDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
Charles Y ChiuDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. charles.chiu@ucsf.edu.ORCID http://orcid.org/0000-0003-2915-2094
University of California, San Francisco · USLeeds Teaching Hospitals NHS Trust · GB

Funding

Engaging University of California Stakeholders for Biorespository ResearchUL1TR000004 · NCATS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GRANDIS, JENNIFER RUBIN · 2012 to 2015
$78.0M
UC BRAID Center for Accelerated Innovation COVID-19 diagnostic project developmentU54HL119893 · NHLBI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI PALAZZOLO, MICHAEL J · 2013 to 2020
$18.3M
Pan-Genomic Approaches for Comprehensive Blood Screening of Novel or Emerging Infectious AgentsR01HL105704 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHIU, CHARLES YEN · 2011 to 2020
$5.9M
Real-Time Unbiased Pathogen Detection in Febrile Illnesses by Nanopore SequencingR33AI120977 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHIU, CHARLES YEN · 2018 to 2020
$1.6M
Illumina Genome Analyzer IIS10RR028106 · NCRR · VANDERBILT UNIVERSITY · PI GEORGE, ALFRED L. · 2011 to 2011
$515k
NCATS NIH HHS UL1 TR000004NCRR NIH HHS S10 RR028106NHLBI NIH HHS R01 HL105704NHLBI NIH HHS U54 HL119893NIAID NIH HHS R33 AI120977U.S. Department of Health & Human Services | National Institutes of Health (NIH) K08-CA230156-01U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI) R01-HL105704U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) R33-AI120977
6 · The paper itself

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.

Indexed as

MetagenomicsAdultAgedBacteriaBody FluidsCell-Free Nucleic AcidsFemaleFungiHigh-Throughput Nucleotide SequencingHumansMaleMiddle AgedCell-Free Nucleic Acids

Identifiers

PMID33169017
PMCPMC9020267
OpenAlexW3099584446

What OpenQuestion holds

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Read underepoch 390

Registered trials

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.