Deep Sequencing of RNA from Blood and Oral Swab Samples Reveals the Presence of Nucleic Acid from a Number of Pathogens in Patients with Acute Ebola Virus Disease and Is Consistent with Bacterial Translocation across the Gut.
Deep Sequencing of RNA from Blood and Oral Swab Samples Reveals the Presence of Nucleic Acid from a Number of Pathogens in Patients with Acute Ebola Virus Disease and Is Consistent with Bacterial Translocation across the Gut.
复制标题
对血液和口腔拭子样品的RNA进行深度测序表明，急性埃博拉病毒疾病患者的许多病原体中存在核酸，并且与整个肠道的细菌易位一致。
DOI：
10.1128/mspheredirect.00325-17
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发表时间：
2017-07
期刊：
影响因子：
4.8
通讯作者：
Hiscox JA
中科院分区：
文献类型：
--
作者：
Carroll MW;Haldenby S;Rickett NY;Pályi B;Garcia-Dorival I;Liu X;Barker G;Bore JA;Koundouno FR;Williamson ED;Laws TR;Kerber R;Sissoko D;Magyar N;Di Caro A;Biava M;Fletcher TE;Sprecher A;Ng LFP;Rénia L;Magassouba N;Günther S;Wölfel R;Stoecker K;Matthews DA;Hiscox JA
我们的结果强调了埃博拉病毒病（EVD）患者血液中一系列病原体的鉴定。这是以前从未做过的，这些数据对埃博拉病毒病患者的治疗具有重要意义，特别是考虑到抗生素管理。我们发现，同时感染疟原虫的埃博拉病毒病患者，尤其是在高负荷情况下，比疟原虫水平较低的患者有更多的不良后果。然而，疟原虫的存在并不影响先天免疫反应，而且埃博拉病毒的存在可能主导了这种反应。还发现了除埃博拉病毒以外的几种病毒，还发现了与败血症相关的细菌。这些发现表明，埃博拉病毒病急性期细菌在肠道内易位。在这项研究中，对 2013 年至 2016 年西非埃博拉病毒爆发时几内亚埃博拉病毒病 (EVD) 患者的样本进行了分析，以发现并分类存在哪些其他病原体。从已故埃博拉病毒病患者身上采集了咽拭子，并对患有急性疾病的患者在治疗中心就诊时采集的外周血样本进行了分析。高通量RNA测序（RNA-seq）和生物信息学被用来鉴定潜在的微生物。这种方法在部署的现场实验室通过定量逆转录 PCR 确诊为病毒急性阳性患者的所有样本中都证实了埃博拉病毒 (EBOV)。疟原虫核酸图谱也用于患者样本，证实了在现场实验室进行的基于抗原的快速诊断测试（RDT）获得的结果。数据表明，由序列读取深度决定的高疟原虫载量与死亡率相关并影响宿主反应，而较低的寄生虫载量似乎并不影响结果。通过 RNA-seq 从咽拭子中鉴定出的选定细菌通过培养得到证实。数据表明，血液样本中发现的潜在病原体与肠道易位有关，表明存在菌血症，转录组数据表明菌血症可能会诱发或加重埃博拉病毒病期间观察到的急性期反应。还鉴定了映射到不同病毒的转录本，包括那些指示裂解性感染的转录本。对埃博拉病毒病患者样本进行高分辨率分析将有助于了解护理途径以及在资源匮乏的环境中使用的最合适的一般抗菌疗法。重要性我们的结果强调了埃博拉病毒病（EVD）患者血液中一系列病原体的鉴定。这是以前从未做过的，这些数据对埃博拉病毒病患者的治疗具有重要意义，特别是考虑到抗生素管理。我们发现，同时感染疟原虫的埃博拉病毒病患者，尤其是在高负荷情况下，比疟原虫水平较低的患者有更多的不良后果。然而，疟原虫的存在并不影响先天免疫反应，而且埃博拉病毒的存在可能主导了这种反应。还发现了除埃博拉病毒以外的几种病毒，还发现了与败血症相关的细菌。这些发现表明，埃博拉病毒病急性期细菌在肠道内易位。
Our results highlight the identification of an array of pathogens in the blood of patients with Ebola virus disease (EVD). This has not been done before, and the data have important implications for the treatment of patients with EVD, particularly considering antibiotic stewardship. We show that EVD patients who were also infected with Plasmodium, particularly at higher loads, had more adverse outcomes than patients with lower levels of Plasmodium. However, the presence of Plasmodium did not influence the innate immune response, and it is likely that the presence of EBOV dominated this response. Several viruses other than EBOV were identified, and bacteria associated with sepsis were also identified. These findings were indicative of bacterial translocation across the gut during the acute phase of EVD. In this study, samples from the 2013–2016 West African Ebola virus outbreak from patients in Guinea with Ebola virus disease (EVD) were analyzed to discover and classify what other pathogens were present. Throat swabs were taken from deceased EVD patients, and peripheral blood samples were analyzed that had been taken from patients when they presented at the treatment center with acute illness. High-throughput RNA sequencing (RNA-seq) and bioinformatics were used to identify the potential microorganisms. This approach confirmed Ebola virus (EBOV) in all samples from patients diagnosed as acute positive for the virus by quantitative reverse transcription-PCR in deployed field laboratories. Nucleic acid mapping to Plasmodium was also used on the patient samples, confirming results obtained with an antigen-based rapid diagnostic test (RDT) conducted in the field laboratories. The data suggested that a high Plasmodium load, as determined by sequence read depth, was associated with mortality and influenced the host response, whereas a lower parasite load did not appear to affect outcome. The identifications of selected bacteria from throat swabs via RNA-seq were confirmed by culture. The data indicated that the potential pathogens identified in the blood samples were associated with translocation from the gut, suggesting the presence of bacteremia, which transcriptome data suggested may induce or aggravate the acute-phase response observed during EVD. Transcripts mapping to different viruses were also identified, including those indicative of lytic infections. The development of high-resolution analysis of samples from patients with EVD will help inform care pathways and the most appropriate general antimicrobial therapy to be used in a resource-poor setting. IMPORTANCE Our results highlight the identification of an array of pathogens in the blood of patients with Ebola virus disease (EVD). This has not been done before, and the data have important implications for the treatment of patients with EVD, particularly considering antibiotic stewardship. We show that EVD patients who were also infected with Plasmodium, particularly at higher loads, had more adverse outcomes than patients with lower levels of Plasmodium. However, the presence of Plasmodium did not influence the innate immune response, and it is likely that the presence of EBOV dominated this response. Several viruses other than EBOV were identified, and bacteria associated with sepsis were also identified. These findings were indicative of bacterial translocation across the gut during the acute phase of EVD.