Yen Ting-Yu, Hsu Ching, Lee Ni-Chung, Wu Chao-Szu, Wang Hsin, Lee Kuan-Yi, Lin Chia-Ray, Lu Chun-Yi, Tsai Mo-Li, Liu Tzu-Yu, Lin Che, Chen Chien-Yu, Chang Luan-Yin, Lai Feipei, Huang Li-Min
Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.
J Microbiol Immunol Infect. 2025 Feb;58(1):86-93. doi: 10.1016/j.jmii.2024.11.011. Epub 2024 Nov 29.
Severe community-acquired pneumonia was associated with high morbidity and mortality in children. However, species-level microbiome of lower airway was sparse, and we used shotgun metagenomic next-generation sequencing to explore microbial signatures.
We conducted a prospective cohort study to recruit children under 18 who required admission to an intensive care unit for community-acquired pneumonia between December 2019 and February 2022. Lower respiratory specimens were collected on admission for shotgun metagenomic sequencing. The children were divided into two groups. Critical cases were patients with respiratory failure requiring endotracheal ventilator support, and severe cases did not require intubation. Signatures of lower respiratory tract microbiome were compared between groups using an exact k-mer matching metagenomic analysis pipeline (Kraken 2) and a metagenome-assembled genomes pipeline (MetaWRAP).
Totally 66 children were enrolled, and 27 children were critical cases, and the rest were severe cases. There were significant differences in microbial community structure between different severity groups, and microbial abundance was negatively correlated with disease severity. The results showed that Haemophilus influenzae was more prominent in children who were critical, accompanied with increased expression of intracellular transport, secretion, and vesicle transport genes. Rothia mucilaginosa, Dolosigranulum pigrum, and Prevotella melaninogenica tended to be present in less severe community-acquired pneumonia group.
This study demonstrated that significantly different microbial community was associated with severity of community-acquired pneumonia requiring intensive care admission. Species-level shotgun metagenomic sequencing facilitates the exploration of potentially pathogenic or protective microbes and shed the light of probiotic development in lower respiratory tract.
重症社区获得性肺炎与儿童的高发病率和死亡率相关。然而，下呼吸道的物种水平微生物组信息匮乏，我们使用鸟枪法宏基因组新一代测序技术来探索微生物特征。
我们进行了一项前瞻性队列研究，招募2019年12月至2022年2月期间因社区获得性肺炎需要入住重症监护病房的18岁以下儿童。入院时采集下呼吸道标本进行鸟枪法宏基因组测序。将儿童分为两组。危重症病例是指需要气管插管呼吸机支持的呼吸衰竭患者，重症病例则不需要插管。使用精确k-mer匹配宏基因组分析流程（Kraken 2）和宏基因组组装基因组流程（MetaWRAP）比较两组下呼吸道微生物组的特征。
共纳入66名儿童，其中27名是危重症病例，其余为重症病例。不同严重程度组之间的微生物群落结构存在显著差异，且微生物丰度与疾病严重程度呈负相关。结果显示，流感嗜血杆菌在危重症儿童中更为突出，同时伴有细胞内运输、分泌和囊泡运输基因表达增加。黏液罗氏菌、嗜麦芽窄食单胞菌和产黑色素普雷沃菌倾向于出现在病情较轻的社区获得性肺炎组。
本研究表明，显著不同的微生物群落与需要入住重症监护病房的社区获得性肺炎的严重程度相关。物种水平的鸟枪法宏基因组测序有助于探索潜在的致病或保护性微生物，并为下呼吸道益生菌的开发提供思路。
