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Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections
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, f...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9684712/ https://www.ncbi.nlm.nih.gov/pubmed/36439227 http://dx.doi.org/10.3389/fcimb.2022.1042945 |
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author | He, Ping Wang, Jing Ke, Rui Zhang, Wei Ning, Pu Zhang, Dexin Yang, Xia Shi, Hongyang Fang, Ping Ming, Zongjuan Li, Wei Zhang, Jie Dong, Xilin Liu, Yun Zhou, Jiemin Xia, Han Yang, Shuanying |
author_facet | He, Ping Wang, Jing Ke, Rui Zhang, Wei Ning, Pu Zhang, Dexin Yang, Xia Shi, Hongyang Fang, Ping Ming, Zongjuan Li, Wei Zhang, Jie Dong, Xilin Liu, Yun Zhou, Jiemin Xia, Han Yang, Shuanying |
author_sort | He, Ping |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9684712 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-96847122022-11-25 Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections He, Ping Wang, Jing Ke, Rui Zhang, Wei Ning, Pu Zhang, Dexin Yang, Xia Shi, Hongyang Fang, Ping Ming, Zongjuan Li, Wei Zhang, Jie Dong, Xilin Liu, Yun Zhou, Jiemin Xia, Han Yang, Shuanying Front Cell Infect Microbiol Cellular and Infection Microbiology 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. Frontiers Media S.A. 2022-11-10 /pmc/articles/PMC9684712/ /pubmed/36439227 http://dx.doi.org/10.3389/fcimb.2022.1042945 Text en Copyright © 2022 He, Wang, Ke, Zhang, Ning, Zhang, Yang, Shi, Fang, Ming, Li, Zhang, Dong, Liu, Zhou, Xia and Yang https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Cellular and Infection Microbiology He, Ping Wang, Jing Ke, Rui Zhang, Wei Ning, Pu Zhang, Dexin Yang, Xia Shi, Hongyang Fang, Ping Ming, Zongjuan Li, Wei Zhang, Jie Dong, Xilin Liu, Yun Zhou, Jiemin Xia, Han Yang, Shuanying Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections |
title | Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections |
title_full | Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections |
title_fullStr | Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections |
title_full_unstemmed | Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections |
title_short | Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections |
title_sort | comparison of metagenomic next-generation sequencing using cell-free dna and whole-cell dna for the diagnoses of pulmonary infections |
topic | Cellular and Infection Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9684712/ https://www.ncbi.nlm.nih.gov/pubmed/36439227 http://dx.doi.org/10.3389/fcimb.2022.1042945 |
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