Pathogen Detection Using Metagenomic Next-Generation Sequencing of Plasma Samples from Patients with Sepsis in Uganda.
Pathogen Detection Using Metagenomic Next-Generation Sequencing of Plasma Samples from Patients with Sepsis in Uganda.
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使用宏基因组下一代测序对乌干达脓毒症患者血浆样本进行病原体检测。
DOI：
10.1128/spectrum.04312-22
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发表时间：
2023-02-14
影响因子：
3.7
通讯作者：
中科院分区：
文献类型：
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作者：
元基因组测序是一种很有前途的病原体检测新方法。我们的目标是使用元基因组测序从存档的血浆中检测病原体，该队列以前具有良好的特征，在乌干达，主要是HIV感染的脓毒症患者。我们使用Illumina测序和Chan Zuckerberg ID元基因组学平台对病原体进行测序和鉴定。平均每个血浆样本产生3,404,737个 ± 2,201,997个读数(平均值±标准差)，其中220,032个 ± 416,691个(6.3%±8.6%)被鉴定为非人类读数。使用背景模型过滤器，在254个样本中发现了414个特定属的病原体鉴定。与测序相比，定量聚合酶链式反应(QPCR)检测出19种病原体呈阳性，敏感性为30.2%，特异性为99.5%。病毒病原体的敏感度高于非病毒病原体(37%对5%)。例如，用定量聚合酶链式反应在69%的样本中检测到艾滋病毒病毒血症，测序显示70%的敏感性和92%的特异性。通过测序，在该队列中发现了75种特定属的潜在病原体，包括乙肝和EB病毒(EBV)等。定量聚合酶链式反应显示，乙肝和EBV病毒血症的患病率分别为17%和45%。住院死亡率与EB病毒较低的qPCR阈值周期有关(调整后的优势比为0.85；P <； .001)，但与乙肝或艾滋病毒无关。总之，在乌干达败血症患者中，通过元基因组测序鉴定出了广泛的潜在病原体。出乎意料的是，乙肝和EBV病毒血症的发生率很高。这些病毒感染在HIV合并脓毒症患者中是否具有临床重要性还有待进一步研究。重要性下一代测序(NGS)在血液样本中的应用是临床微生物学实验室的一项新兴技术。在这项工作中，我们对一个特征明确的队列中的血浆样本进行了NGS，所有样本之前都经过了43种病原体的聚合酶链式反应检测。因此，我们可以将测序性能与聚合酶链式反应进行比较，并确定临床相关性。在乌干达的脓毒症患者中，通过元基因组测序发现了一系列潜在的病原体，特别是病毒，我们通过聚合酶链式反应证实了这一点。除了HIV病毒血症外，还发现了出人意料的高乙肝和EBV病毒血症，这可能具有重要的临床意义。
Metagenomic sequencing is a promising new method for pathogen detection. We aimed to detect pathogens from archived plasma using metagenomic sequencing in a previously well-characterized cohort of 254 predominantly HIV-infected patients with sepsis in Uganda. We used Illumina sequencing and the Chan Zuckerberg ID metagenomics platform to sequence and identify pathogens. On average, each plasma sample yielded 3,404,737 ± 2,201,997 reads (mean ± standard deviation), of which 220,032 ± 416,691 (6.3% ± 8.6%) were identified as nonhuman reads. Using a background model filter, 414 genus-specific pathogen identifications were found in the 254 samples. Nineteen pathogens were previously detected positive by quantitative PCR (qPCR), compared to sequencing, which demonstrated 30.2% sensitivity and 99.5% specificity. Sensitivity was higher for viral pathogens than nonviral pathogens (37% versus 5%). For example, HIV viremia was detected in 69% of samples using qPCR, and sequencing revealed 70% sensitivity and 92% specificity. There were 75 genus-specific potential pathogens identified by sequencing in this cohort, including hepatitis B and Epstein-Barr virus (EBV), among several others. qPCR showed a prevalence of hepatitis B and EBV viremia of 17% and 45%, respectively. In-hospital mortality was associated with a lower qPCR threshold cycle value for EBV (adjusted odds ratio, 0.85; P < .001) but not for hepatitis B or HIV. In conclusion, a broad range of potential pathogens were identified by metagenomic sequencing in patients with sepsis in Uganda. Unexpectedly high rates of hepatitis B and EBV viremia were found. Whether these viral infections in HIV patients with sepsis are clinically important requires further study. IMPORTANCE The use of next-generation sequencing (NGS) in blood samples is an emerging technology for clinical microbiology labs. In this work, we performed NGS on plasma samples from a well-characterized cohort, where all samples had been previously tested by PCR for 43 pathogens. Therefore, we could compare sequencing performance against that of PCR and identify clinical correlates. A broad range of potential pathogens were identified by metagenomic sequencing in patients with sepsis in Uganda, particularly viruses, which we confirmed by PCR. In addition to HIV viremia, unexpectedly high rates of hepatitis B and EBV viremia were found, which may have important clinical implications.
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影响因子：
8.8
作者：
Jacob ST;Banura P;Baeten JM;Moore CC;Meya D;Nakiyingi L;Burke R;Horton CL;Iga B;Wald A;Reynolds SJ;Mayanja-Kizza H;Scheld WM;Promoting Resource-Limited Interventions for Sepsis Management in Uganda Study Group
通讯作者：
Promoting Resource-Limited Interventions for Sepsis Management in Uganda Study Group
DOI：
10.1146/annurev-pathmechdis-012418-012751
发表时间：
2019-01-24
期刊：
Annual review of pathology
影响因子：
--
作者：
Gu W;Miller S;Chiu CY
通讯作者：
Chiu CY
影响因子：
16.6
作者：
通讯作者：
--
影响因子：
9.4
作者：
Morris, T;Robertson, B;Gallagher, M
通讯作者：
Gallagher, M
影响因子：
15.5
作者：
Davis, Nicole M;Proctor, Diana M;Callahan, Benjamin J
通讯作者：
Callahan, Benjamin J