Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system

Post Date: 
2016-06-13
Publication: 
Neurology, Neuroimmunology and Neuroinflammation
Summary: 

OBJECTIVE:

To determine the feasibility of next-generation sequencing (NGS) microbiome approaches in the diagnosis of infectious disorders in brain or spinal cord biopsies in patients with suspected CNS infections.

METHODS:

In a prospective pilot study, we applied NGS in combination with a new computational analysis pipeline to detect the presence of pathogenic microbes in brain or spinal cord biopsies from 10 patients with neurologic problems indicating possible infection but for whom conventional clinical and microbiology studies yielded negative or inconclusive results.

RESULTS:

Direct DNA and RNA sequencing of brain tissue biopsies generated 8.3 million to 29.1 million sequence reads per sample, which successfully identified with high confidence the infectious agent in 3 patients for whom validation techniques confirmed the pathogens identified by NGS. Although NGS was unable to identify with precision infectious agents in the remaining cases, it contributed to the understanding of neuropathologic processes in 5 others, demonstrating the power of large-scale unbiased sequencing as a novel diagnostic tool. Clinical outcomes were consistent with the findings yielded by NGS on the presence or absence of an infectious pathogenic process in 8 of 10 cases, and were noncontributory in the remaining 2.

CONCLUSIONS:

NGS-guided metagenomic studies of brain, spinal cord, or meningeal biopsies offer the possibility for dramatic improvements in our ability to detect (or rule out) a wide range of CNS pathogens, with potential benefits in speed, sensitivity, and cost. NGS-based microbiome approaches present a major new opportunity to investigate the potential role of infectious pathogens in the pathogenesis of neuroinflammatory disorders.

Citation: 
Salzberg SL, Breitwieser FP, Kumar A, Hao H, Burger P, Rodriguez FJ, Lim M, Quiñones-Hinojosa A, Gallia GL, Tornheim JA, Melia MT, Sears CL, Pardo CA. Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system. Neurol Neuroimmunol Neuroinflamm. 2016 Jun 13;3(4):e251. doi: 10.1212/NXI.0000000000000251. eCollection 2016 Aug. PMID: 27340685 PMCID: PMC4907805
Collaborators: 
  • Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine
  • Department of Neurology, Johns Hopkins School of Medicine
  • Deep Sequencing and Microarray Core, Johns Hopkins School of Medicine
  • Department of Pathology, Johns Hopkins School of Medicine
  • Department of Neurosurgery, Johns Hopkins School of Medicine
  • Department of Biomedical Engineering, Johns Hopkins University
  • Department of Computer Science, Johns Hopkins University
  • Deaprtment of Biostatistics, Johns Hopkins University