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Metagenomics for chronic meningitis: clarifying interpretation and diagnosis

Michael R. Wilson M.D., M.A.S., Brian D. O’Donovan M.S., Jeffrey M. Gelfand M.D., M.A.S., Hannah A. Sample B.S., Felicia C. Chow M.D., M.A.S., John P. Betjemann M.D., Maulik P. Shah M.D., Megan B. Richie M.D., Mark P. Gorman M.D., Rula A. Hajj-Ali M.D., Leonard H. Calabrese D.O., Kelsey C. Zorn M.H.S., John E. Greenlee M.D., Jonathan H. Blum M.D., Ph.D., Gary Green M.D., Lillian M. Khan B.S., Debarko Banerji B.S., Charles Langelier M.D., Ph.D., Chloe Bryson-Cahn M.D., Whitney Harrington M.D., Ph.D., Jairam R. Lingappa M.D., Ph.D., Niraj M. Shanbhag M.D., Ph.D., Ari J. Green M.D., M.A.S., Bruce J. Brew M.B.B.S., DMedSci DSc, Ariane Soldatos M.D., Luke Strnad M.D., Sarah B. Doernberg M.D., M.A.S., Cheryl A. Jay M.D., Vanja Douglas M.D., S. Andrew Josephson M.D., Joseph L. DeRisi Ph.D.
doi: https://doi.org/10.1101/213561
Michael R. Wilson M.D., M.A.S.
1UCSF Weill Institute for Neurosciences, San Francisco, CA, USA
2Department of Neurology, University of California, San Francisco, CA, USA
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  • For correspondence: michael.wilson@ucsf.edu
Brian D. O’Donovan M.S.
3Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
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Jeffrey M. Gelfand M.D., M.A.S.
1UCSF Weill Institute for Neurosciences, San Francisco, CA, USA
2Department of Neurology, University of California, San Francisco, CA, USA
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Hannah A. Sample B.S.
3Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
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Felicia C. Chow M.D., M.A.S.
1UCSF Weill Institute for Neurosciences, San Francisco, CA, USA
2Department of Neurology, University of California, San Francisco, CA, USA
4Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, CA, USA
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John P. Betjemann M.D.
1UCSF Weill Institute for Neurosciences, San Francisco, CA, USA
2Department of Neurology, University of California, San Francisco, CA, USA
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Maulik P. Shah M.D.
1UCSF Weill Institute for Neurosciences, San Francisco, CA, USA
2Department of Neurology, University of California, San Francisco, CA, USA
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Megan B. Richie M.D.
1UCSF Weill Institute for Neurosciences, San Francisco, CA, USA
2Department of Neurology, University of California, San Francisco, CA, USA
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Mark P. Gorman M.D.
5Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
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Rula A. Hajj-Ali M.D.
6Department of Rheumatology/Immunology, Cleveland Clinic, Cleveland, Ohio, USA
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Leonard H. Calabrese D.O.
6Department of Rheumatology/Immunology, Cleveland Clinic, Cleveland, Ohio, USA
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Kelsey C. Zorn M.H.S.
3Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
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John E. Greenlee M.D.
7Neurology Service, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
8Department of Neurology, University of Utah Health Sciences Center, Salt Lake City, UT, USA
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Jonathan H. Blum M.D., Ph.D.
9Permanente Medical Group, Oakland, CA, USA
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Gary Green M.D.
9Permanente Medical Group, Oakland, CA, USA
10Santa Rosa Kaiser Medical Center, Santa Rosa, CA, USA
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Lillian M. Khan B.S.
3Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
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Debarko Banerji B.S.
1UCSF Weill Institute for Neurosciences, San Francisco, CA, USA
2Department of Neurology, University of California, San Francisco, CA, USA
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Charles Langelier M.D., Ph.D.
4Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, CA, USA
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Chloe Bryson-Cahn M.D.
11Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
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Whitney Harrington M.D., Ph.D.
12Department of Pediatrics, University of Washington, Seattle, WA, USA
13Seattle Children’s Hospital, Seattle, WA, USA
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Jairam R. Lingappa M.D., Ph.D.
11Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
12Department of Pediatrics, University of Washington, Seattle, WA, USA
14Department of Pediatric Infectious Diseases, Seattle Children’s Hospital, Seattle, WA, USA
15Department of Global Health, University of Washington, Seattle, WA, USA
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Niraj M. Shanbhag M.D., Ph.D.
1UCSF Weill Institute for Neurosciences, San Francisco, CA, USA
2Department of Neurology, University of California, San Francisco, CA, USA
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Ari J. Green M.D., M.A.S.
1UCSF Weill Institute for Neurosciences, San Francisco, CA, USA
2Department of Neurology, University of California, San Francisco, CA, USA
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Bruce J. Brew M.B.B.S., DMedSci DSc
17Neuroscience Program, Peter Duncan Neuroscience Unit, St. Vincent's Hospital Centre for Applied Medical Research Centre, Darlinghurst, NSW Australia
18The University of New South Wales, Sydney, NSW, Australia
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Ariane Soldatos M.D.
19National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services Bethesda, MD, USA
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Luke Strnad M.D.
20Division of Infectious Diseases, Department of Medicine, Oregon Health Sciences University, OR, USA
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Sarah B. Doernberg M.D., M.A.S.
4Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, CA, USA
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Cheryl A. Jay M.D.
1UCSF Weill Institute for Neurosciences, San Francisco, CA, USA
2Department of Neurology, University of California, San Francisco, CA, USA
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Vanja Douglas M.D.
1UCSF Weill Institute for Neurosciences, San Francisco, CA, USA
2Department of Neurology, University of California, San Francisco, CA, USA
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S. Andrew Josephson M.D.
1UCSF Weill Institute for Neurosciences, San Francisco, CA, USA
2Department of Neurology, University of California, San Francisco, CA, USA
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Joseph L. DeRisi Ph.D.
3Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
21Chan Zuckerberg Biohub, San Francisco, CA, USA
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Abstract

Importance Identifying infectious causes of subacute and chronic meningitis can be challenging. Enhanced, unbiased diagnostic approaches are needed.

Objective To present a case series of patients with diagnostically challenging subacute and chronic meningitis in whom metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF), supported by a statistical framework generated from mNGS sequencing of non-infectious patients and environmental controls, identified a pathogen.

Design Case series. Using mNGS data from the CSF of 94 non-infectious neuroinflammatory cases and 24 water and reagent controls, we developed and implemented a weighted scoring metric based on z-scores at the species and genus level for both nucleotide and protein databases to prioritize and rank mNGS results. We performed mNGS on total RNA extracted from CSF of patients with subacute or chronic meningitis and highlight seven cases representing a diverse array of pathogens.

Setting A multi-center study of mNGS pathogen discovery in patients with suspected neuroinflammatory conditions.

Participants Patients with diagnostically challenging subacute or chronic meningitis enrolled in a research study of mNGS performed on CSF.

Intervention mNGS was performed on total RNA extracted from CSF (0.25-0.5 mL). A weighted z-score was used to filter out environmental contaminants and facilitate efficient data triage and analysis.

Main Outcomes 1) Pathogens identified by mNGS and 2) ability of a statistical model to prioritize, rank, and simplify mNGS results.

Results mNGS identified parasitic worms, fungi and viruses in seven subjects: Taenia solium (n=2), Cryptococcus neoformans, human immunodeficiency virus-1, Aspergillus oryzae, Histoplasma capsulatum, and Candida dubliniensis. Evaluating mNGS data with a weighted z-score based scoring algorithm effectively separated bona fide pathogen sequences from spurious environmental sequences.

Conclusions and Relevance mNGS of CSF identified a diversity of microbial pathogens in patients with diagnostically challenging subacute or chronic meningitis, including a case of subarachnoid neurocysticercosis that defied diagnosis for one year, the first case of CNS vasculitis caused by Aspergillus oryzae, and the fourth reported case of Candida dubliniensis meningitis. Filtering metagenomic data with a scoring algorithm greatly clarified data interpretation and highlights the difficulties attributing biological significance to organisms that may be present in control samples used for metagenomic sequencing studies.

Key Points Question: How can metagenomic next-generation sequencing of cerebrospinal fluid be leveraged to aid in the diagnosis of patients with subacute or chronic meningitis?

Findings: Metagenomic next-generation sequencing identified parasitic worms, fungi and viruses in a case series of seven subjects. A database of water-only and healthy patient controls enabled application of a z-score based scoring algorithm to effectively separate bona fide pathogen sequences from spurious environmental sequences.

Meaning: Our scoring algorithm greatly simplified data interpretation in a series of patients with a wide range of challenging infectious causes of subacute or chronic meningitis identified by metagenomic next-generation sequencing.

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.
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Posted November 07, 2017.
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Metagenomics for chronic meningitis: clarifying interpretation and diagnosis
Michael R. Wilson M.D., M.A.S., Brian D. O’Donovan M.S., Jeffrey M. Gelfand M.D., M.A.S., Hannah A. Sample B.S., Felicia C. Chow M.D., M.A.S., John P. Betjemann M.D., Maulik P. Shah M.D., Megan B. Richie M.D., Mark P. Gorman M.D., Rula A. Hajj-Ali M.D., Leonard H. Calabrese D.O., Kelsey C. Zorn M.H.S., John E. Greenlee M.D., Jonathan H. Blum M.D., Ph.D., Gary Green M.D., Lillian M. Khan B.S., Debarko Banerji B.S., Charles Langelier M.D., Ph.D., Chloe Bryson-Cahn M.D., Whitney Harrington M.D., Ph.D., Jairam R. Lingappa M.D., Ph.D., Niraj M. Shanbhag M.D., Ph.D., Ari J. Green M.D., M.A.S., Bruce J. Brew M.B.B.S., DMedSci DSc, Ariane Soldatos M.D., Luke Strnad M.D., Sarah B. Doernberg M.D., M.A.S., Cheryl A. Jay M.D., Vanja Douglas M.D., S. Andrew Josephson M.D., Joseph L. DeRisi Ph.D.
bioRxiv 213561; doi: https://doi.org/10.1101/213561
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Metagenomics for chronic meningitis: clarifying interpretation and diagnosis
Michael R. Wilson M.D., M.A.S., Brian D. O’Donovan M.S., Jeffrey M. Gelfand M.D., M.A.S., Hannah A. Sample B.S., Felicia C. Chow M.D., M.A.S., John P. Betjemann M.D., Maulik P. Shah M.D., Megan B. Richie M.D., Mark P. Gorman M.D., Rula A. Hajj-Ali M.D., Leonard H. Calabrese D.O., Kelsey C. Zorn M.H.S., John E. Greenlee M.D., Jonathan H. Blum M.D., Ph.D., Gary Green M.D., Lillian M. Khan B.S., Debarko Banerji B.S., Charles Langelier M.D., Ph.D., Chloe Bryson-Cahn M.D., Whitney Harrington M.D., Ph.D., Jairam R. Lingappa M.D., Ph.D., Niraj M. Shanbhag M.D., Ph.D., Ari J. Green M.D., M.A.S., Bruce J. Brew M.B.B.S., DMedSci DSc, Ariane Soldatos M.D., Luke Strnad M.D., Sarah B. Doernberg M.D., M.A.S., Cheryl A. Jay M.D., Vanja Douglas M.D., S. Andrew Josephson M.D., Joseph L. DeRisi Ph.D.
bioRxiv 213561; doi: https://doi.org/10.1101/213561

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