Enhanced Virus Detection and Metagenomic Sequencing in Patients with Meningitis and Encephalitis.
Enhanced Virus Detection and Metagenomic Sequencing in Patients with Meningitis and Encephalitis.
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DOI：
10.1128/mbio.01143-21
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发表时间：
2021-08-31
期刊：
影响因子：
6.4
通讯作者：
Sabeti P
中科院分区：
文献类型：
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作者：
Piantadosi A;Mukerji SS;Ye S;Leone MJ;Freimark LM;Park D;Adams G;Lemieux J;Kanjilal S;Solomon IH;Ahmed AA;Goldstein R;Ganesh V;Ostrem B;Cummins KC;Thon JM;Kinsella CM;Rosenberg E;Frosch MP;Goldberg MB;Cho TA;Sabeti P
脑膜炎和脑炎是中枢神经系统（CNS）疾病的主要原因，通常会导致严重的神经功能损害或死亡。传统的诊断工作流程在很大程度上依赖于病原体特异性测试，有时需要几天到几周的时间，而宏基因组下一代测序（mNGS）可以分析样本中的所有核酸。在这项单中心前瞻性研究中，68例已知（n = 44）或疑似（n = 24）CNS感染的住院患者接受了来自RNA和DNA的mNGS，以识别潜在病原体，并使用杂交捕获进行病毒靶向测序。使用基于KrakenUniq和BLAST的计算宏基因组分类管道，我们检测了22名受试者的脑脊液（CSF）中的病原体核酸，其中3名受试者通过常规检查没有临床诊断。在通过血清学和/或外周样本诊断为感染的受试者中，我们证明了mNGS在检测CSF中病原体核酸方面的实用性，特别是对于肩突硬蜱传病原体波瓦桑病毒、伯氏疏螺旋体和嗜吞噬细胞无浆虫。我们还评估了两种增强病毒核酸检测的方法，杂交捕获和甲基化DNA去除。杂交捕获几乎普遍提高了病毒读段回收率。尽管甲基化DNA耗竭的结果是混合的，但它允许在两个通过标准mNGS检测为阴性的样品中检测水痘带状疱疹病毒DNA。总体而言，mNGS是一种有前途的方法，可以同时检测多种病原体，其功效与病原体特异性检测相似，并且可以发现地理相关的传染性CNS疾病，例如新英格兰的蜱媒感染。随着实验室和计算的进一步增强，mNGS可能成为脑炎和脑膜炎检查的支柱。
Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known (n = 44) or suspected (n = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis.