Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology.
Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology.
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缺乏可识别的病因的肺炎儿童中宏基因组学和泛病毒组聚合酶链反应的病毒病原体检测。
DOI：
10.1093/infdis/jix148
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发表时间：
2017-05-01
期刊：
影响因子：
--
通讯作者：
Ampofo K
中科院分区：
文献类型：
--
作者：
Schlaberg R;Queen K;Simmon K;Tardif K;Stockmann C;Flygare S;Kennedy B;Voelkerding K;Bramley A;Zhang J;Eilbeck K;Yandell M;Jain S;Pavia AT;Tong S;Ampofo K
两种广谱病原体检测方法，新一代测序和泛病毒组聚合酶链反应，检测到以前错过了，在34%的儿童社区获得性肺炎住院的假定病原体没有确定的病因。社区获得性肺炎（CAP）是儿科住院的主要原因。病原体鉴定在大约20%的儿童中失败，但对于医院获得性感染的最佳治疗和预防至关重要。我们使用了两种广谱检测策略，以确定病原体检测阴性儿童CAP和无症状对照。通过下一代测序（RNA-seq）和泛病毒组（PVG）PCR检测了来自70名5岁以下不明病因CAP儿童和90名无症状对照的鼻咽/口咽（NP/OP）拭子中19个病毒家族。通过调整的比值比（aOR）和95%置信区间（控制季节和年龄组）评估病毒与CAP的相关性。RNA-seq/PVG PCR在34%的患者中检测到先前遗漏的推定病原体。假定的病毒病原体包括人副流感病毒4型（aOR 9.3，P =.12）、人博卡病毒（aOR 9.1，P <.01）、柯萨奇病毒（aOR 5.1，P =.09）、鼻病毒A（aOR 3.5，P =.34）和鼻病毒C（aOR 2.9，P =.57）。RNA-seq对RNA病毒更敏感，而PVG PCR检测到更多的DNA病毒。RNA-seq和PVG PCR在三分之一因CAP而住院的儿童的NP/OP标本中发现了其他病毒，其中一些已知是致病性的，而这些儿童以前没有确定的病因。这两种广泛的方法可能是有用的工具，在未来的流行病学和诊断研究。
Two broad-spectrum pathogen detection methods, next-generation sequencing and pan-viral group polymerase chain reaction, detected previously missed, putative pathogens in 34% of children hospitalized with community-acquired pneumonia with no identified etiology. Community-acquired pneumonia (CAP) is a leading cause of pediatric hospitalization. Pathogen identification fails in approximately 20% of children but is critical for optimal treatment and prevention of hospital-acquired infections. We used two broad-spectrum detection strategies to identify pathogens in test-negative children with CAP and asymptomatic controls. Nasopharyngeal/oropharyngeal (NP/OP) swabs from 70 children <5 years with CAP of unknown etiology and 90 asymptomatic controls were tested by next-generation sequencing (RNA-seq) and pan viral group (PVG) PCR for 19 viral families. Association of viruses with CAP was assessed by adjusted odds ratios (aOR) and 95% confidence intervals controlling for season and age group. RNA-seq/PVG PCR detected previously missed, putative pathogens in 34% of patients. Putative viral pathogens included human parainfluenza virus 4 (aOR 9.3, P = .12), human bocavirus (aOR 9.1, P < .01), Coxsackieviruses (aOR 5.1, P = .09), rhinovirus A (aOR 3.5, P = .34), and rhinovirus C (aOR 2.9, P = .57). RNA-seq was more sensitive for RNA viruses whereas PVG PCR detected more DNA viruses. RNA-seq and PVG PCR identified additional viruses, some known to be pathogenic, in NP/OP specimens from one-third of children hospitalized with CAP without a previously identified etiology. Both broad-range methods could be useful tools in future epidemiologic and diagnostic studies.
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DOI：
10.1038/nrmicro2949
发表时间：
2013-02
期刊：
Nature reviews. Microbiology
影响因子：
--
作者：
通讯作者：
--
影响因子：
12.7
作者：
Berger, Christoph;Hug, Martina;Nadal, David
通讯作者：
Nadal, David
影响因子：
5.4
作者：
Finkbeiner, Stacy R.;Li, Yan;Tong, Suxiang
通讯作者：
Tong, Suxiang
DOI：
10.1164/rccm.201002-0221oc
发表时间：
2010-11-15
影响因子：
24.7
作者：
DeVincenzo, John P.;Wilkinson, Tom;Lambkin-Williams, Robert
通讯作者：
Lambkin-Williams, Robert
影响因子：
10
作者：
Harris, Michael;Clark, Julia;Thomson, Anne
通讯作者：
Thomson, Anne