Clinical Evaluation of an Improved Metagenomic Next-Generation Sequencing Test for the Diagnosis of Bloodstream Infections
Clinical Evaluation of an Improved Metagenomic Next-Generation Sequencing Test for the Diagnosis of Bloodstream Infections
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DOI：
10.1093/clinchem/hvab061
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发表时间：
2021-06-01
影响因子：
9.3
通讯作者：
Wang, Hui
中科院分区：
文献类型：
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作者：
Jing, Chendi;Chen, Hongbin;Wang, Hui
背景：无浆细胞DNA的新一代宏基因组测序（mNGS）已成为一种有前途的血液感染诊断技术。然而，目前mNGS测定的一个主要限制是由于污染导致的假阳性结果的高比率。方法：我们新颖地采用了长期监测的外部阴性对照、常规检测阴性的血液样本和健康人群3组对照，将其结合起来，专门用于区分标本采集、样品处理和人体正常菌群中产生的污染物。我们还提出了新的标记来过滤假阳性的种间呼叫。该工作流程回顾性应用于209例疑似血流感染患者的临床血浆样本。对mNGS检测确定的每种病原体进行审查，以评估该工作流程的诊断性能。结果：与综合参考标准相比，我们的mNGS工作流程的临床敏感性为87.1%，临床特异性为80.2%，阳性预测值为77.9%，阴性预测值为88.6%。值得注意的是，与目前的检测方法相比，mNGS在保持较高临床敏感性的同时，临床特异性有了很大的提高。结论：具有多个对照组的mNGS工作流程致力于区分非病原微生物和真正的因果病原体，减少了假阳性结果。这一贡献，加上其工作流程的优化和控制的仔细使用，可以帮助mNGS成为识别导致血液感染的病原体的有力工具。
Background: Metagenomic next-generation sequencing (mNGS) of plasma cell-free DNA has emerged as a promising diagnostic technology for bloodstream infections. However, a major limitation of current mNGS assays is the high rate of false-positive results due to contamination.Methods: We made novel use of 3 control groups-external negative controls under long-term surveillance, blood samples with a negative result in conventional tests, and a group of healthy people-that were combined and dedicated to distinguishing contaminants arising from specimen collection, sample processing, and human normal flora. We also proposed novel markers to filter out false-positive interspecies calls. This workflow was applied retrospectively to 209 clinical plasma samples from patients with suspected bloodstream infections. Every pathogen identified by the mNGS test was reviewed to assess the diagnostic performance of the workflow.Results: Our mNGS workflow showed clinical sensitivity of 87.1%, clinical specificity of 80.2%, positive predictive value of 77.9%, and negative predictive value of 88.6% compared with the composite reference standard. Notably, mNGS showed great improvement in clinical specificity compared with the current test while keeping clinical sensitivity at a high level.Conclusion: The mNGS workflow with multiple control groups dedicated to distinguishing nonpathogen microbes from real causal pathogens has reducing false-positive results. This contribution, with its optimization of workflow and careful use of controls, can help mNGS become a powerful tool for identifying the pathogens responsible for bloodstream infections.