Real-world pathogen diagnosis in critically ill infected children: A retrospective study using metagenomic next-generation sequencing with different enrichment strategies

作者：Huili Shen, Xiaolei Zhang, Junfeng Xu, Weike Ma, Wei-Ming Chen, Yixue Wang, Caiyan Zhang, Panpan Fan, Xuemei Zhu, Liming He, Huiyuan Yan, Meili Shen, Guoping Lu, Gangfeng Yan · 发表于：Journal of Infection and Public Health · 年份：2025 · DOI：10.1016/j.jiph.2025.102823 · 研究领域：Genomics and Phylogenetic Studies、Bacterial Identification and Susceptibility Testing、Respiratory viral infections research

BACKGROUND: Study on the clinical pathogen diagnosis in large cohort of critically ill children using metagenomic next-generation sequencing (mNGS) with different enrichment strategies has been limited. METHODS: 763 samples were enrolled and we summarized the clinical pathogen diagnosis and compared the performance between mNGS and clinical microbial tests (CMTs) in different sample types, as well as between shotgun-based (S-mNGS) and hybrid capture-based mNGS (C-mNGS). RESULTS: A total of 93 clinical diagnosed pathogens were identified from763 samples with suspected infections, with a positive rate of 60.16 %. Respiratory specimens had the highest positive rate (90.73 %, 235/259), while the lowest was cerebrospinal fluid (26.94 %, 59/219). mNGS showed higher sensitivity (90.85 % vs. 83.66 %, P = 0.001), specificity (77.30 % vs. 67.43 %, P = 0.007), positive predictive value (PPV, 85.80 % vs. 79.50 %, P = 0.01), negative predictive value (NPV, 84.84 % vs. 73.21 %, P < 0.001), and accuracy (85.45 % vs. 77.20 %, P < 0.001) than CMTs. The corrected true positive rate of mNGS was higher than CMTs (83.88 % vs. 75.60 %, P = 0.002), and its advantage in virus detection was more obvious (OR=1.39, 95 %CI: 1.08-1.78, P = 0.010). S-mNGS and C-mNGS shown significantly higher sensitivity and accuracy than CMTs. However, the total true positive rate between S-mNGS and C-mNGS were close (83.15 % vs. 85.00 %, P = 0.600). According to the mNGS results, the adjusted pathogen diagnosis rate was...