Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections

被引:8
|
作者
He, Ping [1 ]
Wang, Jing [2 ]
Ke, Rui [1 ]
Zhang, Wei [1 ]
Ning, Pu [1 ]
Zhang, Dexin [1 ]
Yang, Xia [1 ]
Shi, Hongyang [1 ]
Fang, Ping [1 ]
Ming, Zongjuan [1 ]
Li, Wei [1 ]
Zhang, Jie [1 ]
Dong, Xilin [1 ]
Liu, Yun [1 ]
Zhou, Jiemin [2 ]
Xia, Han [2 ]
Yang, Shuanying [1 ]
机构
[1] Xi An Jiao Tong Univ, Dept Pulm & Crit Care Med, Affiliated Hosp 2, Xian, Peoples R China
[2] Hugobiotech Co Ltd, Dept Sci Affairs, Beijing, Peoples R China
来源
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY | 2022年 / 12卷
关键词
MNGs; cell-free DNA; whole-cell DNA; pulmonary infection; BALF; PNEUMONIA;
D O I
10.3389/fcimb.2022.1042945
中图分类号
R392 [医学免疫学]; Q939.91 [免疫学];
学科分类号
100102 ;
摘要
Although the fast-growing metagenomic next-generation sequencing (mNGS) has been used in diagnosing infectious diseases, low detection rate of mNGS in detecting pathogens with low loads limits its extensive application. In this study, 130 patients with suspected pulmonary infections were enrolled, from whom bronchoalveolar lavage fluid (BALF) samples were collected. The conventional tests and mNGS of cell-free DNA (cfDNA) and whole-cell DNA (wcDNA) using BALF were simultaneously performed. mNGS of cfDNA showed higher detection rate (91.5%) and total coincidence rate (73.8%) than mNGS of wcDNA (83.1% and 63.9%) and conventional methods (26.9% and 30.8%). A total of 70 microbes were detected by mNGS of cfDNA, and most of them (60) were also identified by mNGS of wcDNA. The 31.8% (21/66) of fungi, 38.6% (27/70) of viruses, and 26.7% (8/30) of intracellular microbes can be only detected by mNGS of cfDNA, much higher than those [19.7% (13/66), 14.3% (10/70), and 6.7% (2/30)] only detected by mNGS of wcDNA. After in-depth analysis on these microbes with low loads set by reads per million (RPM), we found that more RPM and fungi/viruses/intracellular microbes were detected by mNGS of cfDNA than by mNGS of wcDNA. Besides, the abilities of mNGS using both cfDNA and wcDNA to detect microbes with high loads were similar. We highlighted the advantage of mNGS using cfDNA in detecting fungi, viruses, and intracellular microbes with low loads, and suggested that mNGS of cfDNA could be considered as the first choice for diagnosing pulmonary infections.
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页数:11
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