Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
Medical Department, Nanjing Dinfectome Technology Inc., Nanjing, Jiangsu, China.
Front Cell Infect Microbiol. 2023 Aug 15;13:1200806. doi: 10.3389/fcimb.2023.1200806. eCollection 2023.
Metagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection in various infections. In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of pneumonia in pediatric intensive care units (PICU) using bronchoalveolar lavage fluid (BALF) samples.
A total of 104 pediatric patients with pneumonia who were admitted into PICU between June 2018 and February 2020 were retrospectively enrolled. Among them, 101 subjects who had intact clinical information were subject to parallel comparison of mNGS and conventional microbiological tests (CMTs) for pathogen detection. The performance was also evaluated and compared between BALF-mNGS and BALF-culture methods. Moreover, the diversity and structure of all 104 patients' lung BALF microbiomes were explored using the mNGS data.
Combining the findings of mNGS and CMTs, 94.06% (95/101) pneumonia cases showed evidence of causative pathogenic infections, including 79.21% (80/101) mixed and 14.85% (15/101) single infections. Regarding the pathogenesis of pneumonia in the PICU, the fungal detection rates were significantly higher in patients with immunodeficiency (55.56% vs. 25.30%, P =0.025) and comorbidities (40.30% vs. 11.76%, P=0.007). There were no significant differences in the α-diversity either between patients with CAP and HAP or between patients with and without immunodeficiency. Regarding the diagnostic performance, the detection rate of DNA-based BALF-mNGS was slightly higher than that of the BALF-culture although statistically insignificant (81.82% vs.77.92%, P=0.677) and was comparable to CMTs (81.82% vs. 89.61%, P=0.211). The overall sensitivity of DNA-based mNGS was 85.14% (95% confidence interval [CI]: 74.96%-92.34%). The detection rate of RNA-based BALF-mNGS was the same with CMTs (80.00% vs 80.00%, P>0.999) and higher than BALF-culture (80.00% vs 52.00%, P=0.045), with a sensitivity of 90.91% (95%CI: 70.84%-98.88%).
mNGS is valuable in the etiological diagnosis of pneumonia, especially in fungal infections, and can reveal pulmonary microecological characteristics. For pneumonia patients in PICU, the mNGS should be implemented early and complementary to CMTs.
宏基因组下一代测序（mNGS）是一种强大的方法，可用于检测各种感染中的病原体。本研究使用支气管肺泡灌洗液（BALF）样本，评估 mNGS 在儿科重症监护病房（PICU）肺炎的病原体诊断和微生物组分析中的价值。
回顾性纳入 2018 年 6 月至 2020 年 2 月期间入住 PICU 的 104 例肺炎患儿。其中，101 例有完整临床资料的患者并行 mNGS 和常规微生物学检测（CMTs）以检测病原体。评估并比较 BALF-mNGS 和 BALF 培养方法的性能。此外，使用 mNGS 数据探索所有 104 例患者肺部 BALF 微生物组的多样性和结构。
结合 mNGS 和 CMTs 的结果，94.06%（95/101）肺炎病例显示有明确的致病感染证据，包括 79.21%（80/101）混合感染和 14.85%（15/101）单一感染。关于 PICU 肺炎的发病机制，免疫缺陷患儿真菌检出率明显高于无免疫缺陷患儿（55.56% vs. 25.30%，P=0.025）和合并症患儿（40.30% vs. 11.76%，P=0.007）。无论是 CAP 还是 HAP 患儿之间，还是有免疫缺陷和无免疫缺陷患儿之间，α多样性均无显著差异。在诊断性能方面，虽然 DNA 为基础的 BALF-mNGS 的检测率略高于 BALF 培养，但无统计学意义（81.82% vs. 77.92%，P=0.677），与 CMTs 相当（81.82% vs. 89.61%，P=0.211）。DNA 为基础的 mNGS 的总灵敏度为 85.14%（95%置信区间 [CI]：74.96%-92.34%）。RNA 为基础的 BALF-mNGS 的检测率与 CMTs 相同（80.00% vs 80.00%，P＞0.999），高于 BALF 培养（80.00% vs 52.00%，P=0.045），灵敏度为 90.91%（95%CI：70.84%-98.88%）。
mNGS 可用于肺炎的病因诊断，特别是真菌感染，并能揭示肺部微生态特征。对于 PICU 中的肺炎患者，应尽早实施 mNGS，并与 CMTs 互补。
