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April 08, 2014; 82 (10 Supplement) April 29, 2014

Next-Generation Sequencing for Pathogen Discovery in Meningoencephalitis (P2.306)

Michael Wilson, Erik Samayoa, Samia Naccache, Sneha Somasekar, Guixia Yu, Joseph DeRisi, Charles Chiu
First published April 9, 2014,
Michael Wilson
4Neurology University of California San Francisco San Francisco CA United States
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Erik Samayoa
1Laboratory Medicine UCSF San Francisco CA United States
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Samia Naccache
1Laboratory Medicine UCSF San Francisco CA United States
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Sneha Somasekar
1Laboratory Medicine UCSF San Francisco CA United States
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Guixia Yu
1Laboratory Medicine UCSF San Francisco CA United States
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Joseph DeRisi
3Biochemistry and Biophysics University of California San Francisco San Francisco CA United States
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Charles Chiu
2Laboratory Medicine, Internal Medicine UCSF San Francisco CA United States
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Citation
Next-Generation Sequencing for Pathogen Discovery in Meningoencephalitis (P2.306)
Michael Wilson, Erik Samayoa, Samia Naccache, Sneha Somasekar, Guixia Yu, Joseph DeRisi, Charles Chiu
Neurology Apr 2014, 82 (10 Supplement) P2.306;

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Abstract

Objective: Describe a clinical case in which next-generation sequencing (NGS) rapidly identified a rare but treatable bacterial cause of meningoencephalitis resulting in a favorable patient outcome. Background: Over 100 pathogens cause meningoencephalitis, complicating the development of any comprehensive diagnostic workup. Unbiased NGS is revolutionizing our ability to identify new pathogens, especially novel viruses. However, the utility of NGS in the context of critical illness has not been established. Design/Methods: A 14 year-old boy with severe combined immunodeficiency presented with 4 months of headache and fever progressing to hydrocephalus and coma. An exhaustive diagnostic workup including brain biopsy was unrevealing. NGS was performed on the patient’s cerebrospinal fluid (CSF) and blood. The extracted samples were put through a modified TruSeq protocol (Illumina, San Diego, CA) to generate sequencing libraries. The libraries were sequenced on an Illumina MiSeq instrument using 150/350 base pair paired-end sequencing. Using the SNAP nucleotide aligner, the sequences were analyzed using an in-house computational pipeline for viral, bacterial and fungal sequences. Results: The sequencing run yielded 16,375,474 raw reads. In the untreated CSF, 955 reads aligned to the Leptospiraceae bacterial family, and 483 reads aligned to this family in the pre-DNAsed CSF sample. No reads aligned in the pre-DNAsed serum sample. Further analysis showed the reads aligned to Leptospira santarosai with coverage spanning the entire genome. These results were obtained within 48 hours of obtaining the specimens. The Centers for Disease Control's standard PCR assay was negative, but the 16s ribosomal RNA PCR was positive. The patient received appropriate Leptospira anti-microbials and made a dramatic recovery. He is now at home near his pre-morbid baseline. Conclusions: Leptospirosis is a zoonotic bacterial disease that occurs throughout the world. The disease phenotype is widely variable, and meningitis is common. Diagnostic assays for Leptospira are imperfect and rarely pursued. NGS rapidly detected this rare pathogen leading to a dramatic, real-time impact on this patient’s care.

Disclosure: Dr. Wilson has nothing to disclose. Dr. Samayoa has nothing to disclose. Dr. Naccache has nothing to disclose. Dr. Somasekar has nothing to disclose. Dr. Yu has nothing to disclose. Dr. DeRisi has nothing to disclose. Dr. Chiu has nothing to disclose.

Tuesday, April 29 2014, 7:30 am-11:00 am

  • Copyright © 2014 by AAN Enterprises, Inc.

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