Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Laboratory Validation of a Clinical Metagenomic Sequencing Assay for Pathogen Detection in Cerebrospinal Fluid

S Miller, SN Naccache, E Samayoa, K Messacar, S Arevalo, S Federman, D Stryke, E Pham, B Fung, WJ Bolosky, D Ingebrigtsen, W Lorizio, SM Paff, JA Leake, R Pesano, RL DeBiasi, SR Dominguez, View ORCID ProfileCY Chiu
doi: https://doi.org/10.1101/330381
S Miller
1Department of Laboratory Medicine, University of California, San Francisco, San Francisco,CA, USA
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
SN Naccache
1Department of Laboratory Medicine, University of California, San Francisco, San Francisco,CA, USA
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
3Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
E Samayoa
1Department of Laboratory Medicine, University of California, San Francisco, San Francisco,CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
K Messacar
4Department of Pediatrics, Children’s Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
S Arevalo
1Department of Laboratory Medicine, University of California, San Francisco, San Francisco,CA, USA
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
S Federman
1Department of Laboratory Medicine, University of California, San Francisco, San Francisco,CA, USA
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
D Stryke
1Department of Laboratory Medicine, University of California, San Francisco, San Francisco,CA, USA
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
E Pham
1Department of Laboratory Medicine, University of California, San Francisco, San Francisco,CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
B Fung
1Department of Laboratory Medicine, University of California, San Francisco, San Francisco,CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
WJ Bolosky
5Microsoft Research, Redmond, WA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
D Ingebrigtsen
1Department of Laboratory Medicine, University of California, San Francisco, San Francisco,CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
W Lorizio
1Department of Laboratory Medicine, University of California, San Francisco, San Francisco,CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
SM Paff
1Department of Laboratory Medicine, University of California, San Francisco, San Francisco,CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
JA Leake
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
R Pesano
6Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
RL DeBiasi
7Department of Pediatrics, Division of Pediatric Infectious Diseases, Children’s National Health System, Washington, DC, USA
8Department of Pediatrics, Microbiology, Immunology, and Tropical Medicine, The George Washington University School of Medicine, Washington, D.C., USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
SR Dominguez
4Department of Pediatrics, Children’s Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
CY Chiu
1Department of Laboratory Medicine, University of California, San Francisco, San Francisco,CA, USA
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
9Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for CY Chiu
  • For correspondence: charles.chiu@ucsf.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

ABSTRACT

Metagenomic next-generation sequencing (mNGS) for pan-pathogen detection has been successfully tested in proof-of-concept case studies in patients with acute illness of unknown etiology, but to date has been largely confined to research settings. Here we developed and validated an mNGS assay for diagnosis of infectious causes of meningitis and encephalitis from cerebrospinal fluid (CSF) in a licensed clinical laboratory. A clinical bioinformatics pipeline, SURPI+, was developed to rapidly analyze mNGS data, automatically report detected pathogens, and provide a graphical user interface for evaluating and interpreting results. We established quality metrics, threshold values, and limits of detection of between 0.16 – 313 genomic copies or colony forming units per milliliter for each representative organism type. Gross hemolysis and excess host nucleic acid reduced assay sensitivity; however, a spiked phage used as an internal control was a reliable indicator of sensitivity loss. Diagnostic test accuracy was evaluated by blinded mNGS testing of 95 patient samples, revealing 73% sensitivity and 99% specificity compared to original clinical test results, with 81% positive percent agreement and 99% negative percent agreement after discrepancy analysis. Subsequent mNGS challenge testing of 20 positive CSF samples prospectively collected from a cohort of pediatric patients hospitalized with meningitis, myelitis, and/or encephalitis showed 92% sensitivity and 96% specificity relative to conventional microbiological testing of CSF in identifying the causative pathogen. These results demonstrate the analytic performance of a laboratory-validated mNGS assay for pan-pathogen detection, to be used clinically for diagnosis of neurological infections from CSF.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted May 25, 2018.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Laboratory Validation of a Clinical Metagenomic Sequencing Assay for Pathogen Detection in Cerebrospinal Fluid
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Laboratory Validation of a Clinical Metagenomic Sequencing Assay for Pathogen Detection in Cerebrospinal Fluid
S Miller, SN Naccache, E Samayoa, K Messacar, S Arevalo, S Federman, D Stryke, E Pham, B Fung, WJ Bolosky, D Ingebrigtsen, W Lorizio, SM Paff, JA Leake, R Pesano, RL DeBiasi, SR Dominguez, CY Chiu
bioRxiv 330381; doi: https://doi.org/10.1101/330381
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Laboratory Validation of a Clinical Metagenomic Sequencing Assay for Pathogen Detection in Cerebrospinal Fluid
S Miller, SN Naccache, E Samayoa, K Messacar, S Arevalo, S Federman, D Stryke, E Pham, B Fung, WJ Bolosky, D Ingebrigtsen, W Lorizio, SM Paff, JA Leake, R Pesano, RL DeBiasi, SR Dominguez, CY Chiu
bioRxiv 330381; doi: https://doi.org/10.1101/330381

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3701)
  • Biochemistry (7827)
  • Bioengineering (5699)
  • Bioinformatics (21354)
  • Biophysics (10607)
  • Cancer Biology (8212)
  • Cell Biology (11982)
  • Clinical Trials (138)
  • Developmental Biology (6790)
  • Ecology (10427)
  • Epidemiology (2065)
  • Evolutionary Biology (13912)
  • Genetics (9733)
  • Genomics (13114)
  • Immunology (8176)
  • Microbiology (20077)
  • Molecular Biology (7882)
  • Neuroscience (43187)
  • Paleontology (321)
  • Pathology (1285)
  • Pharmacology and Toxicology (2269)
  • Physiology (3365)
  • Plant Biology (7259)
  • Scientific Communication and Education (1317)
  • Synthetic Biology (2012)
  • Systems Biology (5551)
  • Zoology (1135)