Evidence map›Paper›PMID 27562436›Full record

ArticleGenome medicine2016

Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens.

Thuy Doan, Michael R Wilson, Emily D Crawford, Eric D Chow, Lillian M Khan, Kristeene A Knopp, Brian D O'Donovan, Dongxiang Xia, Jill K Hacker, Jay M Stewart and 3 more

Erratum issuedOpen access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome medicine, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 110 papers, 3 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
110citing papers in PubMed, 3 pooled it
19.5field-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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

110 citing papers in PubMed, 3 syntheses or guidelines pooled it, 206 citations in OpenAlex.

  1. Pooled it
  2. Pooled it
  3. Guideline
  4. Trial
  5. Reduction of Coronavirus Burden With Mass Azithromycin Distribution.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2020
    Trial
  6. Trial
  7. Review
  8. Article
  9. 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
  10. Integrative analysis of SEC13: a prognostic predictor and immunotherapeutic target.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026
    Article
  11. Current perspective on infectious uveitis.Indian journal of ophthalmology · 2026
    Review
  12. Article
  13. Article
  14. Review
  15. Article
  16. Article
  17. Delayed-onsetAmerican journal of ophthalmology case reports · 2025
    Article
  18. Article
  19. Review
  20. Review

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

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors at 3 institutions in 1 country.

Thuy DoanFrancis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA.
Michael R WilsonDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
Emily D CrawfordDepartment of Biochemistry and Biophysics, 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.
Lillian M KhanDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
Kristeene A KnoppDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
Brian D O'DonovanDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
Dongxiang XiaCalifornia Department of Public Health, Richmond, CA, USA.
Jill K HackerCalifornia Department of Public Health, Richmond, CA, USA.
Jay M StewartDepartment of Ophthalmology, University of California San Francisco, San Francisco, CA, USA.
John A GonzalesFrancis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA.
Nisha R AcharyaFrancis I. Proctor Foundation, 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. joe@derisilab.ucsf.edu.
University of California, San Francisco · USCalifornia Department of Public Health · USSan Francisco Foundation · US

Funding

Rapid-Prototyping and Design CoreP30EY002162 · NEI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LAMBA, DEEPAK ASHOK · 1985 to 2024
$16.8M
Clinical and Transtional Science InstituteKL2TR000143 · NCATS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GRANDIS, JENNIFER RUBIN · 2012 to 2015
$11.9M
BMI Bioinformatics Training GrantsT32GM067547 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HERNANDEZ, RYAN D. · 2003 to 2022
$6.6M
Ocular Surface Microbiome, Virome, and Pathogens in Ophthalmic Disease and HealthK08EY026986 · NEI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI DOAN, THUY A · 2016 to 2020
$1.2M
NCATS NIH HHS KL2 TR000143NEI NIH HHS K08 EY026986NIGMS NIH HHS T32 GM067547OSELS CDC HHS U60 OE000103
6 · The paper itself

Abstract

backgroundOcular infections remain a major cause of blindness and morbidity worldwide. While prognosis is dependent on the timing and accuracy of diagnosis, the etiology remains elusive in ~50 % of presumed infectious uveitis cases. The objective of this study is to determine if unbiased metagenomic deep sequencing (MDS) can accurately detect pathogens in intraocular fluid samples of patients with uveitis.

methodsThis is a proof-of-concept study, in which intraocular fluid samples were obtained from five subjects with known diagnoses, and one subject with bilateral chronic uveitis without a known etiology. Samples were subjected to MDS, and results were compared with those from conventional diagnostic tests. Pathogens were identified using a rapid computational pipeline to analyze the non-host sequences obtained from MDS.

resultsUnbiased MDS of intraocular fluid produced results concordant with known diagnoses in subjects with (n = 4) and without (n = 1) uveitis. Samples positive for Cryptococcus neoformans, Toxoplasma gondii, and herpes simplex virus 1 as tested by a Clinical Laboratory Improvement Amendments-certified laboratory were correctly identified with MDS. Rubella virus was identified in one case of chronic bilateral idiopathic uveitis. The subject's strain was most closely related to a German rubella virus strain isolated in 1992, one year before he developed a fever and rash while living in Germany. The pattern and the number of viral identified mutations present in the patient's strain were consistent with long-term viral replication in the eye.

conclusionsMDS can identify fungi, parasites, and DNA and RNA viruses in minute volumes of intraocular fluid samples. The identification of chronic intraocular rubella virus infection highlights the eye's role as a long-term pathogen reservoir, which has implications for virus eradication and emerging global epidemics.

Indexed as

MetagenomicsAqueous HumorCryptococcosisCryptococcus neoformansHerpes SimplexHerpesvirus 1, HumanHigh-Throughput Nucleotide SequencingHumansPhylogenyRubellaRubella virusToxoplasmaToxoplasmosisUveaUveitisVirus ReplicationMetagenomic deep sequencingPathogen discoveryRubella virusUveitis

Identifiers

PMID27562436
PMCPMC4997733
OpenAlexW2513861476

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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.