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...
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Autor*in:	Ping He [verfasserIn] Jing Wang [verfasserIn] Rui Ke [verfasserIn] Wei Zhang [verfasserIn] Pu Ning [verfasserIn] Dexin Zhang [verfasserIn] Xia Yang [verfasserIn] Hongyang Shi [verfasserIn] Ping Fang [verfasserIn] Zongjuan Ming [verfasserIn] Wei Li [verfasserIn] Jie Zhang [verfasserIn] Xilin Dong [verfasserIn] Yun Liu [verfasserIn] Jiemin Zhou [verfasserIn] Han Xia [verfasserIn] Shuanying Yang [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2022

Schlagwörter:	MNGs cell-free DNA whole-cell DNA pulmonary infection BALF

Übergeordnetes Werk:	In: Frontiers in Cellular and Infection Microbiology - Frontiers Media S.A., 2016, 12(2022)
Übergeordnetes Werk:	volume:12 ; year:2022

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3389/fcimb.2022.1042945

Katalog-ID:	DOAJ020852444

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520			\|a 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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allfields	10.3389/fcimb.2022.1042945 doi (DE-627)DOAJ020852444 (DE-599)DOAJc312673f814248489d340912988a83a3 DE-627 ger DE-627 rakwb eng QR1-502 Ping He verfasserin aut Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. MNGs cell-free DNA whole-cell DNA pulmonary infection BALF Microbiology Jing Wang verfasserin aut Rui Ke verfasserin aut Wei Zhang verfasserin aut Pu Ning verfasserin aut Dexin Zhang verfasserin aut Xia Yang verfasserin aut Hongyang Shi verfasserin aut Ping Fang verfasserin aut Zongjuan Ming verfasserin aut Wei Li verfasserin aut Jie Zhang verfasserin aut Xilin Dong verfasserin aut Yun Liu verfasserin aut Jiemin Zhou verfasserin aut Han Xia verfasserin aut Shuanying Yang verfasserin aut In Frontiers in Cellular and Infection Microbiology Frontiers Media S.A., 2016 12(2022) (DE-627)664968554 (DE-600)2619676-1 22352988 nnns volume:12 year:2022 https://doi.org/10.3389/fcimb.2022.1042945 kostenfrei https://doaj.org/article/c312673f814248489d340912988a83a3 kostenfrei https://www.frontiersin.org/articles/10.3389/fcimb.2022.1042945/full kostenfrei https://doaj.org/toc/2235-2988 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2022
spelling	10.3389/fcimb.2022.1042945 doi (DE-627)DOAJ020852444 (DE-599)DOAJc312673f814248489d340912988a83a3 DE-627 ger DE-627 rakwb eng QR1-502 Ping He verfasserin aut Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. MNGs cell-free DNA whole-cell DNA pulmonary infection BALF Microbiology Jing Wang verfasserin aut Rui Ke verfasserin aut Wei Zhang verfasserin aut Pu Ning verfasserin aut Dexin Zhang verfasserin aut Xia Yang verfasserin aut Hongyang Shi verfasserin aut Ping Fang verfasserin aut Zongjuan Ming verfasserin aut Wei Li verfasserin aut Jie Zhang verfasserin aut Xilin Dong verfasserin aut Yun Liu verfasserin aut Jiemin Zhou verfasserin aut Han Xia verfasserin aut Shuanying Yang verfasserin aut In Frontiers in Cellular and Infection Microbiology Frontiers Media S.A., 2016 12(2022) (DE-627)664968554 (DE-600)2619676-1 22352988 nnns volume:12 year:2022 https://doi.org/10.3389/fcimb.2022.1042945 kostenfrei https://doaj.org/article/c312673f814248489d340912988a83a3 kostenfrei https://www.frontiersin.org/articles/10.3389/fcimb.2022.1042945/full kostenfrei https://doaj.org/toc/2235-2988 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2022
allfields_unstemmed	10.3389/fcimb.2022.1042945 doi (DE-627)DOAJ020852444 (DE-599)DOAJc312673f814248489d340912988a83a3 DE-627 ger DE-627 rakwb eng QR1-502 Ping He verfasserin aut Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. MNGs cell-free DNA whole-cell DNA pulmonary infection BALF Microbiology Jing Wang verfasserin aut Rui Ke verfasserin aut Wei Zhang verfasserin aut Pu Ning verfasserin aut Dexin Zhang verfasserin aut Xia Yang verfasserin aut Hongyang Shi verfasserin aut Ping Fang verfasserin aut Zongjuan Ming verfasserin aut Wei Li verfasserin aut Jie Zhang verfasserin aut Xilin Dong verfasserin aut Yun Liu verfasserin aut Jiemin Zhou verfasserin aut Han Xia verfasserin aut Shuanying Yang verfasserin aut In Frontiers in Cellular and Infection Microbiology Frontiers Media S.A., 2016 12(2022) (DE-627)664968554 (DE-600)2619676-1 22352988 nnns volume:12 year:2022 https://doi.org/10.3389/fcimb.2022.1042945 kostenfrei https://doaj.org/article/c312673f814248489d340912988a83a3 kostenfrei https://www.frontiersin.org/articles/10.3389/fcimb.2022.1042945/full kostenfrei https://doaj.org/toc/2235-2988 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2022
allfieldsGer	10.3389/fcimb.2022.1042945 doi (DE-627)DOAJ020852444 (DE-599)DOAJc312673f814248489d340912988a83a3 DE-627 ger DE-627 rakwb eng QR1-502 Ping He verfasserin aut Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. MNGs cell-free DNA whole-cell DNA pulmonary infection BALF Microbiology Jing Wang verfasserin aut Rui Ke verfasserin aut Wei Zhang verfasserin aut Pu Ning verfasserin aut Dexin Zhang verfasserin aut Xia Yang verfasserin aut Hongyang Shi verfasserin aut Ping Fang verfasserin aut Zongjuan Ming verfasserin aut Wei Li verfasserin aut Jie Zhang verfasserin aut Xilin Dong verfasserin aut Yun Liu verfasserin aut Jiemin Zhou verfasserin aut Han Xia verfasserin aut Shuanying Yang verfasserin aut In Frontiers in Cellular and Infection Microbiology Frontiers Media S.A., 2016 12(2022) (DE-627)664968554 (DE-600)2619676-1 22352988 nnns volume:12 year:2022 https://doi.org/10.3389/fcimb.2022.1042945 kostenfrei https://doaj.org/article/c312673f814248489d340912988a83a3 kostenfrei https://www.frontiersin.org/articles/10.3389/fcimb.2022.1042945/full kostenfrei https://doaj.org/toc/2235-2988 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2022
allfieldsSound	10.3389/fcimb.2022.1042945 doi (DE-627)DOAJ020852444 (DE-599)DOAJc312673f814248489d340912988a83a3 DE-627 ger DE-627 rakwb eng QR1-502 Ping He verfasserin aut Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. MNGs cell-free DNA whole-cell DNA pulmonary infection BALF Microbiology Jing Wang verfasserin aut Rui Ke verfasserin aut Wei Zhang verfasserin aut Pu Ning verfasserin aut Dexin Zhang verfasserin aut Xia Yang verfasserin aut Hongyang Shi verfasserin aut Ping Fang verfasserin aut Zongjuan Ming verfasserin aut Wei Li verfasserin aut Jie Zhang verfasserin aut Xilin Dong verfasserin aut Yun Liu verfasserin aut Jiemin Zhou verfasserin aut Han Xia verfasserin aut Shuanying Yang verfasserin aut In Frontiers in Cellular and Infection Microbiology Frontiers Media S.A., 2016 12(2022) (DE-627)664968554 (DE-600)2619676-1 22352988 nnns volume:12 year:2022 https://doi.org/10.3389/fcimb.2022.1042945 kostenfrei https://doaj.org/article/c312673f814248489d340912988a83a3 kostenfrei https://www.frontiersin.org/articles/10.3389/fcimb.2022.1042945/full kostenfrei https://doaj.org/toc/2235-2988 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2022
language	English
source	In Frontiers in Cellular and Infection Microbiology 12(2022) volume:12 year:2022
sourceStr	In Frontiers in Cellular and Infection Microbiology 12(2022) volume:12 year:2022
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	MNGs cell-free DNA whole-cell DNA pulmonary infection BALF Microbiology
isfreeaccess_bool	true
container_title	Frontiers in Cellular and Infection Microbiology
authorswithroles_txt_mv	Ping He @@aut@@ Jing Wang @@aut@@ Rui Ke @@aut@@ Wei Zhang @@aut@@ Pu Ning @@aut@@ Dexin Zhang @@aut@@ Xia Yang @@aut@@ Hongyang Shi @@aut@@ Ping Fang @@aut@@ Zongjuan Ming @@aut@@ Wei Li @@aut@@ Jie Zhang @@aut@@ Xilin Dong @@aut@@ Yun Liu @@aut@@ Jiemin Zhou @@aut@@ Han Xia @@aut@@ Shuanying Yang @@aut@@
publishDateDaySort_date	2022-01-01T00:00:00Z
hierarchy_top_id	664968554
id	DOAJ020852444
language_de	englisch
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callnumber-first	Q - Science
author	Ping He
spellingShingle	Ping He misc QR1-502 misc MNGs misc cell-free DNA misc whole-cell DNA misc pulmonary infection misc BALF misc Microbiology Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections
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topic_title	QR1-502 Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections MNGs cell-free DNA whole-cell DNA pulmonary infection BALF
topic	misc QR1-502 misc MNGs misc cell-free DNA misc whole-cell DNA misc pulmonary infection misc BALF misc Microbiology
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title	Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections
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title_full	Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections
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author_browse	Ping He Jing Wang Rui Ke Wei Zhang Pu Ning Dexin Zhang Xia Yang Hongyang Shi Ping Fang Zongjuan Ming Wei Li Jie Zhang Xilin Dong Yun Liu Jiemin Zhou Han Xia Shuanying Yang
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title_sort	comparison of metagenomic next-generation sequencing using cell-free dna and whole-cell dna for the diagnoses of pulmonary infections
callnumber	QR1-502
title_auth	Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections
abstract	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.
abstractGer	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.
abstract_unstemmed	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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title_short	Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections
url	https://doi.org/10.3389/fcimb.2022.1042945 https://doaj.org/article/c312673f814248489d340912988a83a3 https://www.frontiersin.org/articles/10.3389/fcimb.2022.1042945/full https://doaj.org/toc/2235-2988
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author2	Jing Wang Rui Ke Wei Zhang Pu Ning Dexin Zhang Xia Yang Hongyang Shi Ping Fang Zongjuan Ming Wei Li Jie Zhang Xilin Dong Yun Liu Jiemin Zhou Han Xia Shuanying Yang
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up_date	2024-07-03T17:23:33.477Z
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Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections

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