Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China.
Clin Infect Dis. 2020 Dec 23;71(Suppl 4):S416-S426. doi: 10.1093/cid/ciaa1516.
Only few pathogens that cause lower respiratory tract infections (LRTIs) can be identified due to limitations of traditional microbiological methods and the complexity of the oropharyngeal normal flora. Metagenomic next-generation sequencing (mNGS) has the potential to solve this problem.
This prospective observational study sequentially enrolled 93 patients with LRTI and 69 patients without LRTI who visited Peking University People's Hospital in 2019. Pathogens in bronchoalveolar lavage fluid (BALF) specimens were detected using mNGS (DNA and RNA) and traditional microbiological assays. Human transcriptomes were compared between LRTI and non-LRTI, bacterial and viral LRTI, and tuberculosis and nontuberculosis groups.
Among 93 patients with LRTI, 20%, 35%, and 65% of cases were detected as definite or probable pathogens by culture, all microbiological tests, and mNGS, respectively. Our in-house BALF mNGS platform had an approximately 2-working-day turnaround time and detected more viruses and fungi than the other methods. Taking the composite reference standard as a gold standard, it had a sensitivity of 66.7%, specificity of 75.4%, positive-predictive value of 78.5%, and negative-predictive value of 62.7%. LRTI-, viral LRTI-, and tuberculosis-related differentially expressed genes were respectively related to immunity responses to infection, viral transcription and response to interferon-γ pathways, and perforin 1 and T-cell receptor B variable 9.
Metagenomic DNA and RNA-seq can identify a wide range of LRTI pathogens, with improved sensitivity for viruses and fungi. Our in-host platform is likely feasible in the clinic. Host transcriptome data are expected to be useful for the diagnosis of LRTIs.
由于传统微生物方法的局限性和口咽部正常菌群的复杂性，仅有少数能引起下呼吸道感染（LRTIs）的病原体可以被识别。宏基因组下一代测序（mNGS）有可能解决这个问题。
本前瞻性观察性研究于 2019 年连续纳入了 93 例 LRTI 患者和 69 例无 LRTI 患者。使用 mNGS（DNA 和 RNA）和传统微生物检测方法检测支气管肺泡灌洗液（BALF）标本中的病原体。比较 LRTI 和非 LRTI、细菌性和病毒性 LRTI 以及结核和非结核组之间的人转录组。
在 93 例 LRTI 患者中，培养、所有微生物检测和 mNGS 分别检测到 20%、35%和 65%的病例为明确或可能的病原体。我们内部的 BALF mNGS 平台的周转时间约为 2 个工作日，比其他方法检测到更多的病毒和真菌。以综合参考标准为金标准，其灵敏度为 66.7%，特异性为 75.4%，阳性预测值为 78.5%，阴性预测值为 62.7%。LRTI、病毒性 LRTI 和结核病相关差异表达基因分别与感染免疫反应、病毒转录和干扰素-γ途径反应以及穿孔素 1 和 T 细胞受体 B 可变 9 相关。
宏基因组 DNA 和 RNA-seq 可识别广泛的 LRTI 病原体，对病毒和真菌的敏感性提高。我们的宿主内平台在临床上可能是可行的。宿主转录组数据有望用于 LRTIs 的诊断。
