Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens.
Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens.
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DOI：
10.1186/s13073-016-0344-6
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发表时间：
2016-08-25
期刊：
影响因子：
12.3
通讯作者：
DeRisi JL
中科院分区：
文献类型：
--
作者：
Doan T;Wilson MR;Crawford ED;Chow ED;Khan LM;Knopp KA;O'Donovan BD;Xia D;Hacker JK;Stewart JM;Gonzales JA;Acharya NR;DeRisi JL
眼部感染仍然是全世界失明和发病的主要原因。虽然预后取决于诊断的时机和准确性，但在约50%的假定感染性葡萄膜炎病例中，病因仍然难以确定。本研究的目的是确定无偏宏基因组深度测序（MDS）是否可以准确检测葡萄膜炎患者眼内液样本中的病原体。这是一项概念验证研究，其中从5名诊断已知的受试者和1名病因不明的双侧慢性葡萄膜炎受试者中获得眼内液样本。样本进行MDS，并与常规诊断试验的结果进行比较。使用快速计算管道来分析从MDS获得的非宿主序列来鉴定病原体。眼内液的无偏倚MDS在患有（n = 4）和不患有（n = 1）葡萄膜炎的受试者中产生与已知诊断一致的结果。经临床实验室改进修正案认证的实验室检测，新生隐球菌、刚地弓形虫和单纯疱疹病毒1型阳性的样本被正确鉴定为MDS。风疹病毒被确定在一个慢性双侧特发性葡萄膜炎的情况下。该受试者的病毒株与1992年分离的德国风疹病毒株最密切相关，一年后，他在德国生活时出现发烧和皮疹。患者菌株中存在的病毒鉴定突变的模式和数量与眼睛中的长期病毒复制一致。MDS可以识别微量眼内液样本中的真菌、寄生虫、DNA和RNA病毒。慢性眼内风疹病毒感染的鉴定突出了眼睛作为长期病原体储存库的作用，这对病毒根除和新出现的全球流行病具有影响。本文的在线版本（doi：10.1186/s13073-016-0344-6）包含补充材料，可供授权用户使用。
Ocular infections remain a major cause of blindness and morbidity worldwide. While prognosis is dependent on the timing and accuracy of diagnosis, the etiology remains elusive in ~50 % of presumed infectious uveitis cases. The objective of this study is to determine if unbiased metagenomic deep sequencing (MDS) can accurately detect pathogens in intraocular fluid samples of patients with uveitis. This is a proof-of-concept study, in which intraocular fluid samples were obtained from five subjects with known diagnoses, and one subject with bilateral chronic uveitis without a known etiology. Samples were subjected to MDS, and results were compared with those from conventional diagnostic tests. Pathogens were identified using a rapid computational pipeline to analyze the non-host sequences obtained from MDS. Unbiased MDS of intraocular fluid produced results concordant with known diagnoses in subjects with (n = 4) and without (n = 1) uveitis. Samples positive for Cryptococcus neoformans, Toxoplasma gondii, and herpes simplex virus 1 as tested by a Clinical Laboratory Improvement Amendments-certified laboratory were correctly identified with MDS. Rubella virus was identified in one case of chronic bilateral idiopathic uveitis. The subject’s strain was most closely related to a German rubella virus strain isolated in 1992, one year before he developed a fever and rash while living in Germany. The pattern and the number of viral identified mutations present in the patient’s strain were consistent with long-term viral replication in the eye. MDS can identify fungi, parasites, and DNA and RNA viruses in minute volumes of intraocular fluid samples. The identification of chronic intraocular rubella virus infection highlights the eye’s role as a long-term pathogen reservoir, which has implications for virus eradication and emerging global epidemics. The online version of this article (doi:10.1186/s13073-016-0344-6) contains supplementary material, which is available to authorized users.