Metagenomic analysis using next-generation sequencing of pathogens in bronchoalveolar lavage fluid from pediatric patients with respiratory failure
Metagenomic analysis using next-generation sequencing of pathogens in bronchoalveolar lavage fluid from pediatric patients with respiratory failure
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DOI：
10.1038/s41598-019-49372-x
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发表时间：
2019-09-09
影响因子：
4.6
通讯作者：
Ito, Yoshinori
中科院分区：
文献类型：
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作者：
Takeuchi, Suguru;Kawada, Jun-ichi;Ito, Yoshinori
新一代测序技术已在传染病领域得到广泛应用。支气管肺泡灌洗液（BALF）被认为是一种无菌类型的标本，适合于检测呼吸道感染的病原体。本研究的目的是利用NGS在免疫功能正常的呼吸衰竭患儿的BALF样本中全面鉴定致病病原体。纳入10例因呼吸衰竭住院的患者。急性期获得的BALF样本用于制备dna和rna测序文库。利用MiSeq对文库进行测序，利用宏基因组分析工具对序列数据进行分析。每个文库平均有2,041,216个reads被测序。10名患者中有8名检测到显著的细菌或病毒测序读数。此外，候选病原体在3例患者中检测到病原未被常规方法确定。在两例患者中鉴定出肠道病毒D68的全基因组，系统发育分析表明，这两种菌株都属于B3亚支系，这是近年来在世界范围内传播的一种流行毒株。结果表明，NGS可用于呼吸道感染患者BALF的综合分子诊断和病原体监测。
Next-generation sequencing (NGS) has been applied in the field of infectious diseases. Bronchoalveolar lavage fluid (BALF) is considered a sterile type of specimen that is suitable for detecting pathogens of respiratory infections. The aim of this study was to comprehensively identify causative pathogens using NGS in BALF samples from immunocompetent pediatric patients with respiratory failure. Ten patients hospitalized with respiratory failure were included. BALF samples obtained in the acute phase were used to prepare DNA-and RNA-sequencing libraries. The libraries were sequenced on MiSeq, and the sequence data were analyzed using metagenome analysis tools. A mean of 2,041,216 total reads were sequenced for each library. Significant bacterial or viral sequencing reads were detected in eight of the 10 patients. Furthermore, candidate pathogens were detected in three patients in whom etiologic agents were not identified by conventional methods. The complete genome of enterovirus D68 was identified in two patients, and phylogenetic analysis suggested that both strains belong to subclade B3, which is an epidemic strain that has spread worldwide in recent years. Our results suggest that NGS can be applied for comprehensive molecular diagnostics as well as surveillance of pathogens in BALF from patients with respiratory infection.