Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine (S.L.S., F.P.B.), Department of Neurology (A.K., C.A.P.), Deep Sequencing and Microarray Core (H.H.), and Departments of Pathology (P.B., F.J.R., C.A.P.), Neurosurgery (M.L., A.Q.-H., G.L.G.), and Medicine (J.A.T., M.T.M., C.L.S.), School of Medicine, and Departments of Biomedical Engineering, Computer Science, and Biostatistics (S.L.S.), Johns Hopkins University, Baltimore, MD.
Neurol Neuroimmunol Neuroinflamm. 2016 Jun 13;3(4):e251. doi: 10.1212/NXI.0000000000000251. eCollection 2016 Aug.
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.
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.
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.
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.
确定下一代测序 (NGS) 微生物组方法在诊断疑似中枢神经系统感染患者的脑或脊髓活检中感染性疾病的可行性。
在一项前瞻性试点研究中，我们应用 NGS 结合新的计算分析管道来检测 10 名有神经问题的患者脑或脊髓活检中致病性微生物的存在，这些患者的神经问题表明可能存在感染，但常规临床和微生物学研究结果为阴性或不确定。
直接对脑组织活检进行 DNA 和 RNA 测序，每个样本产生 830 万到 2910 万条序列，成功地在 3 名患者中以高可信度识别出了病原体，验证技术证实了 NGS 鉴定的病原体。尽管 NGS 无法准确识别其余病例中的感染性病原体，但它有助于理解 5 名患者的神经病理过程，展示了大规模无偏测序作为一种新的诊断工具的强大功能。在 10 例中的 8 例中，临床结果与 NGS 检测到或未检测到感染性致病过程的结果一致，其余 2 例结果无帮助。
对脑、脊髓或脑膜活检进行 NGS 指导的宏基因组研究有可能极大地提高我们检测（或排除）广泛中枢神经系统病原体的能力，在速度、灵敏度和成本方面具有潜在优势。基于 NGS 的微生物组方法为研究感染性病原体在神经炎症性疾病发病机制中的潜在作用提供了一个重大的新机会。
