背景:肺炎通常由多种病原微生物引起。传统的研究通常集中在少数微生物的感染上,而宏基因组学研究的重点是细菌组和分枝杆菌对呼吸道疾病的影响。关于小儿肺炎病毒学特征的报道仍然相对较少。
方法:我们采用从头组装和基于同源和特征的组合方法来表征口咽(OP)拭子的全基因组DNA测序样品中的呼吸道病毒,鼻咽(NP)拭子,肺炎患儿的支气管肺泡灌洗液(BALF)。
结果:在α和β多样性指数中观察到显着差异,以及口咽病毒的组成,在肺炎病例和对照之间。我们确定了1137个具有显著差异的病毒操作分类单位(vOTU),表明肺炎减少的vOTUs倾向于感染普雷沃氏菌,奈瑟菌,还有Veillonella,而富含肺炎的vOTU包括多瘤病毒,人腺病毒,和针对葡萄球菌的噬菌体,链球菌,肉芽肿,放线菌。比较分析显示,与减少肺炎的vOTUs相比,NP和BALF样本中富含肺炎的OPvOTUs的相对丰度和患病率更高。此外,病毒学分析确定了六名患有严重人类腺病毒或多瘤病毒感染的儿科患者,其中5人可能未被靶向聚合酶链反应(PCR)检测.
结论:这项研究提供了对小儿肺炎呼吸道病毒,强调潜在致病性病毒的频繁传播,并证明病毒学分析是病原体检测的有价值的辅助手段。
BACKGROUND: Pneumonia is typically caused by a variety of pathogenic microorganisms. Traditional research often focuses on the infection of a few microorganisms, whereas metagenomic studies focus on the impact of the bacteriome and mycobiome on respiratory diseases. Reports on the
virome characteristics of pediatric pneumonia remain relatively scarce.
METHODS: We employed de novo assembly and combined homology- and feature-based methods to characterize the respiratory
virome in whole-genome DNA sequencing samples from oropharynx (OP) swabs, nasopharynx (NP) swabs, and bronchoalveolar lavage fluids (BALF) of children with pneumonia.
RESULTS: Significant differences were observed in the alpha and beta diversity indexes, as well as in the composition of the oropharyngeal
virome, between pneumonia cases and controls. We identified 1137 viral operational taxonomic units (vOTUs) with significant differences, indicating a preference of pneumonia-reduced vOTUs for infecting Prevotella, Neisseria, and Veillonella, whereas pneumonia-enriched vOTUs included polyomavirus, human adenovirus, and phages targeting Staphylococcus, Streptococcus, Granulicatella, and Actinomyces. Comparative analysis revealed higher relative abundances and prevalence rates of pneumonia-enriched OP vOTUs in NP and BALF samples compared to pneumonia-reduced vOTUs. Additionally,
virome analysis identified six pediatric patients with severe human adenovirus or polyomavirus infections, five of whom might have been undetected by targeted polymerase chain reaction (PCR)-based testing.
CONCLUSIONS: This study offers insights into pediatric pneumonia respiratory viromes, highlighting frequent transmission of potentially pathogenic viruses and demonstrating
virome analysis as a valuable adjunct for pathogen detection.