Comprehensive pathogen detection for ocular infections.
Comprehensive pathogen detection for ocular infections.
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DOI：
10.1016/j.jcv.2021.104759
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发表时间：
2021-03
期刊：
影响因子：
--
通讯作者：
Acharya NR
中科院分区：
文献类型：
--
作者：
Doan T;Sahoo MK;Ruder K;Huang C;Zhong L;Chen C;Hinterwirth A;Lin C;Gonzales JA;Pinsky BA;Acharya NR
自20世纪90年代末以来，病原体导向PCR等分子诊断技术已经改变了眼部感染的检测方法。尽管这些测定仍然是用于具有低生物量的样品的重要诊断工具，但是诊断范围的缺乏激发了用于眼部感染的替代分子方法。本研究的目的是确定高通量RNA测序方法RNA-seq的性能，以检测疑似眼部感染患者眼部样本中的感染因子。我们比较了RNA-seq与病原体导向PCR的性能，使用来自41例疑似眼部感染患者的房水或玻璃体样本的残留核酸。在CLIA认证的斯坦福大学临床病毒学实验室进行病原体定向PCR。RNA-seq在弗朗西斯科大学的加州普罗克特基金会以掩蔽方式进行。计算两种检测方法之间的阳性和阴性一致性百分比。对不一致的结果进行正交试验。RNA-seq和病原体定向PCR之间的阳性百分比一致性为100%（95%置信区间（CI）：78.5%至100%）。阴性一致率为92.6%（95% CI：76.6%-97.9%）。RNA-seq在9.7%（4/41）的样本中鉴定出未进行鉴别诊断的病原体。用正交试验证实了仅用RNA-seq鉴定的两种病原体。RNA-seq可以准确地识别疑似眼部感染患者的房水和玻璃体样本中的常见和罕见病原体。这种无偏见的测试方法有可能改善诊断，尽管实际的临床效用需要更多的研究。
Molecular diagnostics such as pathogen-directed PCRs have transformed testing for ocular infections since the late 1990s. Although these assays remain important diagnostic tools for samples with low biomass, the lack of diagnostic range motivates alternative molecular approaches for ocular infections. The aim of this study was to determine the performance of a high-throughput RNA sequencing approach, RNA-seq, to detect infectious agents in ocular samples from patients with presumed ocular infections. We compared the performance of RNA-seq to pathogen-directed PCRs using remnant nucleic acids from 41 aqueous or vitreous samples of patients with presumed ocular infections. Pathogen-directed PCRs were performed at the CLIA-certified Stanford Clinical Virology Laboratory. RNA-seq was performed in a masked manner at the Proctor Foundation at the University of California San Francisco. Percent positive and negative agreement between the two testing approaches were calculated. Discordant results were subjected to orthogonal testing. The positive percent agreement between RNA-seq and pathogen-directed PCRs was 100% (95% confidence interval (CI): 78.5% to 100%). The negative percent agreement was 92.6% (95% CI: 76.6% to 97.9%). RNA-seq identified pathogens not on the differential diagnosis for 9.7% (4/41) of the samples. Two pathogens solely identified with RNA-seq were confirmed with orthogonal testing. RNA-seq can accurately identify common and rare pathogens in aqueous and vitreous samples of patients with presumed ocular infections. Such an unbiased approach to testing has the potential to improve diagnostics although practical clinical utility warrants additional studies.
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影响因子：
13.7
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
通讯作者：
DeRisi JL
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
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：
7
作者：
Muthappan, Valliammai;Lee, Aaron Y.;Van Gelder, Russell N.
通讯作者：
Van Gelder, Russell N.
影响因子：
7
作者：
Kim D;Song L;Breitwieser FP;Salzberg SL
通讯作者：
Salzberg SL