Metagenomic DNA Sequencing for the Diagnosis of Intraocular Infections.
Metagenomic DNA Sequencing for the Diagnosis of Intraocular Infections.
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DOI：
10.1016/j.ophtha.2017.03.045
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发表时间：
2017-08
期刊：
影响因子：
13.7
通讯作者：
DeRisi JL
中科院分区：
文献类型：
--
作者：
Doan T;Acharya NR;Pinsky BA;Sahoo MK;Chow ED;Banaei N;Budvytiene I;Cevallos V;Zhong L;Zhou Z;Lietman TM;DeRisi JL
眼内感染的检测在很大程度上依赖于分子诊断。一个根本性的挑战是，在任何给定时间只能安全地获得100-300 μl的眼内液用于诊断测试。眼科感染的最广泛可用的分子诊断面板包括4个单独的病原体定向聚合酶链反应（PCR）：巨细胞病毒（CMV），单纯疱疹病毒（HSV），水痘带状疱疹病毒（VZV）和弓形虫。毫不奇怪，超过50%的所有假定的眼内感染未能确定病原体。1宏基因组深度测序具有提高诊断率的潜力，因为它是无偏和无假设的;理论上它可以检测临床样本中的所有病原体。2，3之前，我们证明了眼内液的无偏RNA测序（RNA-seq）可以检测葡萄膜炎患者中的真菌，寄生虫，DNA和RNA病毒。2关于RNA-seq的一个明显的缺点是，最佳的RNA测序需要适当的标本处理，包括快速冷冻或立即将标本置于干冰上。虽然商业室温RNA防腐剂可以解决这个问题，执业眼科医生可能会发现这些收集技术在门诊设置不切实际。对于具有DNA基因组的病原体，宏基因组DNA测序（DNA-seq）可以规避这一挑战，因为DNA对环境温度的耐受性更强。本研究比较了DNA-seq与传统病原体导向PCR诊断眼内感染的性能。
Detection of intraocular infections relies heavily on molecular diagnostics. A fundamental challenge is that only 100–300 μl of intraocular fluid can be safely obtained at any given time for diagnostic testing. The most widely available molecular diagnostic panel for infections in ophthalmology includes 4 separate pathogen-directed polymerase chain reactions (PCRs): cytomegalovirus (CMV), herpes simplex virus (HSV), varicella zoster virus (VZV), and Toxoplasma gondii. Not surprisingly, more than 50% of all presumed intraocular infections fail to have a pathogen identified. 1Metagenomic deep sequencing has the potential to improve diagnostic yield as it is unbiased and hypothesis-free; it can theoretically detect all pathogens in a clinical sample. 2, 3 Previously, we demonstrated that unbiased RNA sequencing (RNA-seq) of intraocular fluid detects fungi, parasites, DNA and RNA viruses in uveitis patients. 2 One obvious drawback regarding RNA-seq is that optimal RNA sequencing requires proper specimen handling, including either flash-freezing or immediate placement of the specimen on dry ice. Although commercial room-temperature RNA-preservatives may address this issue, practicing ophthalmologists may find these collection techniques impractical in an outpatient setting. For pathogens with DNA genomes, metagenomic DNA sequencing (DNA-seq) can circumvent this challenge, as DNA is more tolerant of ambient temperature. This study compares the performance of DNA-seq with conventional pathogen-directed PCRs to diagnose intraocular infections.
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影响因子：
12.3
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
通讯作者：
DeRisi JL
影响因子：
3.2
作者：
Brunetto, Giovanna S.;Massoud, Raya;Leibovitch, Emily C.;Caruso, Breanna;Johnson, Kory;Ohayon, Joan;Fenton, Kaylan;Cortese, Irene;Jacobson, Steven
通讯作者：
Jacobson, Steven
影响因子：
9.4
作者：
Sahoo, Malaya K.;Lefterova, Martina I.;Pinsky, Benjamin A.
通讯作者：
Pinsky, Benjamin A.
影响因子：
9.4
作者：
Graf, Erin H.;Simmon, Keith E.;Schlaberg, Robert
通讯作者：
Schlaberg, Robert