Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
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
_version_ 1784835351637917696
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
work_keys_str_mv AT heping comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT wangjing comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT kerui comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT zhangwei comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT ningpu comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT zhangdexin comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT yangxia comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT shihongyang comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT fangping comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT mingzongjuan comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT liwei comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT zhangjie comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT dongxilin comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT liuyun comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT zhoujiemin comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT xiahan comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections
AT yangshuanying comparisonofmetagenomicnextgenerationsequencingusingcellfreednaandwholecelldnaforthediagnosesofpulmonaryinfections