Performance of targeted next-generation sequencing in the detection of respiratory pathogens and antimicrobial resistance genes for children

作者：R. V. T. P. Lin, Zhihao Xing, Xiaorong Liu, Qiang Chai, Zefeng Xin, Meng Huang, Chunqing Zhu, Ce Luan, Hongdan Gao, Yao Du, Xuwen Deng, Hetong Zhang, Dongli Ma · 发表于：Journal of Medical Microbiology · 年份：2023 · DOI：10.1099/jmm.0.001771 · 被引用次数：49 · 研究领域：Respiratory viral infections research、Pneumonia and Respiratory Infections、Microbial infections and disease research

Introduction. Respiratory tract infection, which is associated with high morbidity and mortality, occurs frequently in children. At present, the main diagnostic method is culture. However, the low pathogen detection rate of the culture approach prevents timely and accurate diagnosis. Fortunately, next-generation sequencing (NGS) can compensate for the deficiency of culture, and its application in clinical diagnostics has become increasingly available. Gap Statement. Targeted NGS (tNGS) is a platform that can select and enrich specific regions before data enter the NGS pipeline. However, the performance of tNGS in the detection of respiratory pathogens and antimicrobial resistance genes (ARGs) in infections in children is unclear. Aim and methodology. In this study, we estimated the performance of tNGS in the detection of respiratory pathogens and ARGs in 47 bronchoalveolar lavage fluid (BALF) specimens from children using conventional culture and antimicrobial susceptibility testing (AST) as the gold standard. Results. RPIP (Respiratory Pathogen ID/AMR enrichment) sequencing generated almost 500 000 reads for each specimen. In the detection of pathogens, RPIP sequencing showed targeted superiority in detecting difficult-to-culture bacteria, including Mycoplasma pneumoniae . Compared with the results of culture, the sensitivity and specificity of RPIP were 84.4 % (confidence interval 70.5–93.5 %) and 97.7 % (95.9 –98.8%), respectively. Moreover, RPIP results showed that a sing...