Abstract
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.
Highlights
In the field of infectious diseases, identification of etiologic microorganisms is essential for definitive diagnosis and decisions regarding appropriate management
bronchoalveolar lavage fluid (BALF)-2 was obtained from a 6-monthold patient with extremely low birth weight and chronic lung disease, and Serratia marcescens was isolated from a transtracheal aspiration sample
In BALF-1, the total number of bacterial reads obtained from the library prepared with the Microbiome kit (MB kit) was more than 100 times higher than that with the Path kit
Summary
In the field of infectious diseases, identification of etiologic microorganisms is essential for definitive diagnosis and decisions regarding appropriate management. Virus isolation is a reliable method to determine the causative pathogen, but it is time-consuming, and its sensitivity may be insufficient. Combinations of these procedures are performed, no significant pathogens are identified in 34–57% of pediatric patients[1] and 13–62% of adult patients with pneumonia[2,3]. Sputum is generally used for detecting pathogens that cause lower respiratory tract infections. Miao et al have shown that significant reads of candidate pathogens were detected in 34% of BALF samples obtained from patients with infectious and noninfectious diseases[21].
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