Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infectious Pathogens From Bronchoalveolar Lavage Samples

BackgroundMetagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection. In this study, we assessed the value of mNGS for bronchoalveolar lavage (BAL) samples in the diagnosis of pulmonary infections.MethodsFrom February 2018 to April 2019, BAL samples were collected from...
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Autor*in:	Yuqian Chen [verfasserIn] Wei Feng [verfasserIn] Kai Ye [verfasserIn] Li Guo [verfasserIn] Han Xia [verfasserIn] Yuanlin Guan [verfasserIn] Limin Chai [verfasserIn] Wenhua Shi [verfasserIn] Cui Zhai [verfasserIn] Jian Wang [verfasserIn] Xin Yan [verfasserIn] Qingting Wang [verfasserIn] Qianqian Zhang [verfasserIn] Cong Li [verfasserIn] Pengtao Liu [verfasserIn] Manxiang Li [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2021

Schlagwörter:	metagenomic next-generation sequencing (mNGS) bronchoalveolar lavage fluid (BALF) pulmonary infection etiological culture diagnostic

Übergeordnetes Werk:	In: Frontiers in Cellular and Infection Microbiology - Frontiers Media S.A., 2016, 11(2021)
Übergeordnetes Werk:	volume:11 ; year:2021

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3389/fcimb.2021.541092

Katalog-ID:	DOAJ049713019

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520			\|a BackgroundMetagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection. In this study, we assessed the value of mNGS for bronchoalveolar lavage (BAL) samples in the diagnosis of pulmonary infections.MethodsFrom February 2018 to April 2019, BAL samples were collected from 235 patients with suspected pulmonary infections. mNGS and microbial culture were performed to evaluate the effectiveness of mNGS in pulmonary infection diagnosis.ResultsWe employed mNGS to evaluate the alpha diversity, results suggesting that patients with confirmed pathogens had a lower microbial diversity index compared to that of patients with uncertain pathogens. For the patients admitted to the respiratory intensive care unit (RICU) or on a ventilator, they experienced a lower diversity index than that of the patients in the general ward or not on a ventilator. In addition, mNGS of BAL had a diagnostic sensitivity of 88.89% and a specificity of 14.86% in pulmonary infection, with 21.16% positive predictive value (PPV) and 83.87% negative predictive value (NPV). When rare pathogens were excluded, the sensitivity of mNGS decreased to 73.33%, and the specificity increased to 41.71%. For patients in the simple pulmonary infection group and the immunocompromised group, the main infection types were bacterial infection (58.33%) and mixed-infection (43.18%). Furthermore, mNGS had an advantage over culture in describing polymicrobial ecosystem, demonstrating the microbial distribution and the dominant strains of the respiratory tract in patients with different underlying diseases.ConclusionsThe study indicated that mNGS of BAL samples could provide more accurate diagnostic information in pulmonary infections and demonstrate the changes of respiratory microbiome in different underlying diseases. This method might play an important role in the clinical use of antimicrobial agents in the future.
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allfields	10.3389/fcimb.2021.541092 doi (DE-627)DOAJ049713019 (DE-599)DOAJ7a2ca6c4c27c447da37de9028771fe95 DE-627 ger DE-627 rakwb eng QR1-502 Yuqian Chen verfasserin aut Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infectious Pathogens From Bronchoalveolar Lavage Samples 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier BackgroundMetagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection. In this study, we assessed the value of mNGS for bronchoalveolar lavage (BAL) samples in the diagnosis of pulmonary infections.MethodsFrom February 2018 to April 2019, BAL samples were collected from 235 patients with suspected pulmonary infections. mNGS and microbial culture were performed to evaluate the effectiveness of mNGS in pulmonary infection diagnosis.ResultsWe employed mNGS to evaluate the alpha diversity, results suggesting that patients with confirmed pathogens had a lower microbial diversity index compared to that of patients with uncertain pathogens. For the patients admitted to the respiratory intensive care unit (RICU) or on a ventilator, they experienced a lower diversity index than that of the patients in the general ward or not on a ventilator. In addition, mNGS of BAL had a diagnostic sensitivity of 88.89% and a specificity of 14.86% in pulmonary infection, with 21.16% positive predictive value (PPV) and 83.87% negative predictive value (NPV). When rare pathogens were excluded, the sensitivity of mNGS decreased to 73.33%, and the specificity increased to 41.71%. For patients in the simple pulmonary infection group and the immunocompromised group, the main infection types were bacterial infection (58.33%) and mixed-infection (43.18%). Furthermore, mNGS had an advantage over culture in describing polymicrobial ecosystem, demonstrating the microbial distribution and the dominant strains of the respiratory tract in patients with different underlying diseases.ConclusionsThe study indicated that mNGS of BAL samples could provide more accurate diagnostic information in pulmonary infections and demonstrate the changes of respiratory microbiome in different underlying diseases. This method might play an important role in the clinical use of antimicrobial agents in the future. metagenomic next-generation sequencing (mNGS) bronchoalveolar lavage fluid (BALF) pulmonary infection etiological culture diagnostic Microbiology Wei Feng verfasserin aut Kai Ye verfasserin aut Li Guo verfasserin aut Han Xia verfasserin aut Yuanlin Guan verfasserin aut Limin Chai verfasserin aut Wenhua Shi verfasserin aut Cui Zhai verfasserin aut Jian Wang verfasserin aut Xin Yan verfasserin aut Qingting Wang verfasserin aut Qianqian Zhang verfasserin aut Cong Li verfasserin aut Pengtao Liu verfasserin aut Manxiang Li verfasserin aut In Frontiers in Cellular and Infection Microbiology Frontiers Media S.A., 2016 11(2021) (DE-627)664968554 (DE-600)2619676-1 22352988 nnns volume:11 year:2021 https://doi.org/10.3389/fcimb.2021.541092 kostenfrei https://doaj.org/article/7a2ca6c4c27c447da37de9028771fe95 kostenfrei https://www.frontiersin.org/articles/10.3389/fcimb.2021.541092/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 11 2021
spelling	10.3389/fcimb.2021.541092 doi (DE-627)DOAJ049713019 (DE-599)DOAJ7a2ca6c4c27c447da37de9028771fe95 DE-627 ger DE-627 rakwb eng QR1-502 Yuqian Chen verfasserin aut Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infectious Pathogens From Bronchoalveolar Lavage Samples 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier BackgroundMetagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection. In this study, we assessed the value of mNGS for bronchoalveolar lavage (BAL) samples in the diagnosis of pulmonary infections.MethodsFrom February 2018 to April 2019, BAL samples were collected from 235 patients with suspected pulmonary infections. mNGS and microbial culture were performed to evaluate the effectiveness of mNGS in pulmonary infection diagnosis.ResultsWe employed mNGS to evaluate the alpha diversity, results suggesting that patients with confirmed pathogens had a lower microbial diversity index compared to that of patients with uncertain pathogens. For the patients admitted to the respiratory intensive care unit (RICU) or on a ventilator, they experienced a lower diversity index than that of the patients in the general ward or not on a ventilator. In addition, mNGS of BAL had a diagnostic sensitivity of 88.89% and a specificity of 14.86% in pulmonary infection, with 21.16% positive predictive value (PPV) and 83.87% negative predictive value (NPV). When rare pathogens were excluded, the sensitivity of mNGS decreased to 73.33%, and the specificity increased to 41.71%. For patients in the simple pulmonary infection group and the immunocompromised group, the main infection types were bacterial infection (58.33%) and mixed-infection (43.18%). Furthermore, mNGS had an advantage over culture in describing polymicrobial ecosystem, demonstrating the microbial distribution and the dominant strains of the respiratory tract in patients with different underlying diseases.ConclusionsThe study indicated that mNGS of BAL samples could provide more accurate diagnostic information in pulmonary infections and demonstrate the changes of respiratory microbiome in different underlying diseases. This method might play an important role in the clinical use of antimicrobial agents in the future. metagenomic next-generation sequencing (mNGS) bronchoalveolar lavage fluid (BALF) pulmonary infection etiological culture diagnostic Microbiology Wei Feng verfasserin aut Kai Ye verfasserin aut Li Guo verfasserin aut Han Xia verfasserin aut Yuanlin Guan verfasserin aut Limin Chai verfasserin aut Wenhua Shi verfasserin aut Cui Zhai verfasserin aut Jian Wang verfasserin aut Xin Yan verfasserin aut Qingting Wang verfasserin aut Qianqian Zhang verfasserin aut Cong Li verfasserin aut Pengtao Liu verfasserin aut Manxiang Li verfasserin aut In Frontiers in Cellular and Infection Microbiology Frontiers Media S.A., 2016 11(2021) (DE-627)664968554 (DE-600)2619676-1 22352988 nnns volume:11 year:2021 https://doi.org/10.3389/fcimb.2021.541092 kostenfrei https://doaj.org/article/7a2ca6c4c27c447da37de9028771fe95 kostenfrei https://www.frontiersin.org/articles/10.3389/fcimb.2021.541092/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 11 2021
allfields_unstemmed	10.3389/fcimb.2021.541092 doi (DE-627)DOAJ049713019 (DE-599)DOAJ7a2ca6c4c27c447da37de9028771fe95 DE-627 ger DE-627 rakwb eng QR1-502 Yuqian Chen verfasserin aut Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infectious Pathogens From Bronchoalveolar Lavage Samples 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier BackgroundMetagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection. In this study, we assessed the value of mNGS for bronchoalveolar lavage (BAL) samples in the diagnosis of pulmonary infections.MethodsFrom February 2018 to April 2019, BAL samples were collected from 235 patients with suspected pulmonary infections. mNGS and microbial culture were performed to evaluate the effectiveness of mNGS in pulmonary infection diagnosis.ResultsWe employed mNGS to evaluate the alpha diversity, results suggesting that patients with confirmed pathogens had a lower microbial diversity index compared to that of patients with uncertain pathogens. For the patients admitted to the respiratory intensive care unit (RICU) or on a ventilator, they experienced a lower diversity index than that of the patients in the general ward or not on a ventilator. In addition, mNGS of BAL had a diagnostic sensitivity of 88.89% and a specificity of 14.86% in pulmonary infection, with 21.16% positive predictive value (PPV) and 83.87% negative predictive value (NPV). When rare pathogens were excluded, the sensitivity of mNGS decreased to 73.33%, and the specificity increased to 41.71%. For patients in the simple pulmonary infection group and the immunocompromised group, the main infection types were bacterial infection (58.33%) and mixed-infection (43.18%). Furthermore, mNGS had an advantage over culture in describing polymicrobial ecosystem, demonstrating the microbial distribution and the dominant strains of the respiratory tract in patients with different underlying diseases.ConclusionsThe study indicated that mNGS of BAL samples could provide more accurate diagnostic information in pulmonary infections and demonstrate the changes of respiratory microbiome in different underlying diseases. This method might play an important role in the clinical use of antimicrobial agents in the future. metagenomic next-generation sequencing (mNGS) bronchoalveolar lavage fluid (BALF) pulmonary infection etiological culture diagnostic Microbiology Wei Feng verfasserin aut Kai Ye verfasserin aut Li Guo verfasserin aut Han Xia verfasserin aut Yuanlin Guan verfasserin aut Limin Chai verfasserin aut Wenhua Shi verfasserin aut Cui Zhai verfasserin aut Jian Wang verfasserin aut Xin Yan verfasserin aut Qingting Wang verfasserin aut Qianqian Zhang verfasserin aut Cong Li verfasserin aut Pengtao Liu verfasserin aut Manxiang Li verfasserin aut In Frontiers in Cellular and Infection Microbiology Frontiers Media S.A., 2016 11(2021) (DE-627)664968554 (DE-600)2619676-1 22352988 nnns volume:11 year:2021 https://doi.org/10.3389/fcimb.2021.541092 kostenfrei https://doaj.org/article/7a2ca6c4c27c447da37de9028771fe95 kostenfrei https://www.frontiersin.org/articles/10.3389/fcimb.2021.541092/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 11 2021
allfieldsGer	10.3389/fcimb.2021.541092 doi (DE-627)DOAJ049713019 (DE-599)DOAJ7a2ca6c4c27c447da37de9028771fe95 DE-627 ger DE-627 rakwb eng QR1-502 Yuqian Chen verfasserin aut Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infectious Pathogens From Bronchoalveolar Lavage Samples 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier BackgroundMetagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection. In this study, we assessed the value of mNGS for bronchoalveolar lavage (BAL) samples in the diagnosis of pulmonary infections.MethodsFrom February 2018 to April 2019, BAL samples were collected from 235 patients with suspected pulmonary infections. mNGS and microbial culture were performed to evaluate the effectiveness of mNGS in pulmonary infection diagnosis.ResultsWe employed mNGS to evaluate the alpha diversity, results suggesting that patients with confirmed pathogens had a lower microbial diversity index compared to that of patients with uncertain pathogens. For the patients admitted to the respiratory intensive care unit (RICU) or on a ventilator, they experienced a lower diversity index than that of the patients in the general ward or not on a ventilator. In addition, mNGS of BAL had a diagnostic sensitivity of 88.89% and a specificity of 14.86% in pulmonary infection, with 21.16% positive predictive value (PPV) and 83.87% negative predictive value (NPV). When rare pathogens were excluded, the sensitivity of mNGS decreased to 73.33%, and the specificity increased to 41.71%. For patients in the simple pulmonary infection group and the immunocompromised group, the main infection types were bacterial infection (58.33%) and mixed-infection (43.18%). Furthermore, mNGS had an advantage over culture in describing polymicrobial ecosystem, demonstrating the microbial distribution and the dominant strains of the respiratory tract in patients with different underlying diseases.ConclusionsThe study indicated that mNGS of BAL samples could provide more accurate diagnostic information in pulmonary infections and demonstrate the changes of respiratory microbiome in different underlying diseases. This method might play an important role in the clinical use of antimicrobial agents in the future. metagenomic next-generation sequencing (mNGS) bronchoalveolar lavage fluid (BALF) pulmonary infection etiological culture diagnostic Microbiology Wei Feng verfasserin aut Kai Ye verfasserin aut Li Guo verfasserin aut Han Xia verfasserin aut Yuanlin Guan verfasserin aut Limin Chai verfasserin aut Wenhua Shi verfasserin aut Cui Zhai verfasserin aut Jian Wang verfasserin aut Xin Yan verfasserin aut Qingting Wang verfasserin aut Qianqian Zhang verfasserin aut Cong Li verfasserin aut Pengtao Liu verfasserin aut Manxiang Li verfasserin aut In Frontiers in Cellular and Infection Microbiology Frontiers Media S.A., 2016 11(2021) (DE-627)664968554 (DE-600)2619676-1 22352988 nnns volume:11 year:2021 https://doi.org/10.3389/fcimb.2021.541092 kostenfrei https://doaj.org/article/7a2ca6c4c27c447da37de9028771fe95 kostenfrei https://www.frontiersin.org/articles/10.3389/fcimb.2021.541092/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 11 2021
allfieldsSound	10.3389/fcimb.2021.541092 doi (DE-627)DOAJ049713019 (DE-599)DOAJ7a2ca6c4c27c447da37de9028771fe95 DE-627 ger DE-627 rakwb eng QR1-502 Yuqian Chen verfasserin aut Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infectious Pathogens From Bronchoalveolar Lavage Samples 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier BackgroundMetagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection. In this study, we assessed the value of mNGS for bronchoalveolar lavage (BAL) samples in the diagnosis of pulmonary infections.MethodsFrom February 2018 to April 2019, BAL samples were collected from 235 patients with suspected pulmonary infections. mNGS and microbial culture were performed to evaluate the effectiveness of mNGS in pulmonary infection diagnosis.ResultsWe employed mNGS to evaluate the alpha diversity, results suggesting that patients with confirmed pathogens had a lower microbial diversity index compared to that of patients with uncertain pathogens. For the patients admitted to the respiratory intensive care unit (RICU) or on a ventilator, they experienced a lower diversity index than that of the patients in the general ward or not on a ventilator. In addition, mNGS of BAL had a diagnostic sensitivity of 88.89% and a specificity of 14.86% in pulmonary infection, with 21.16% positive predictive value (PPV) and 83.87% negative predictive value (NPV). When rare pathogens were excluded, the sensitivity of mNGS decreased to 73.33%, and the specificity increased to 41.71%. For patients in the simple pulmonary infection group and the immunocompromised group, the main infection types were bacterial infection (58.33%) and mixed-infection (43.18%). Furthermore, mNGS had an advantage over culture in describing polymicrobial ecosystem, demonstrating the microbial distribution and the dominant strains of the respiratory tract in patients with different underlying diseases.ConclusionsThe study indicated that mNGS of BAL samples could provide more accurate diagnostic information in pulmonary infections and demonstrate the changes of respiratory microbiome in different underlying diseases. This method might play an important role in the clinical use of antimicrobial agents in the future. metagenomic next-generation sequencing (mNGS) bronchoalveolar lavage fluid (BALF) pulmonary infection etiological culture diagnostic Microbiology Wei Feng verfasserin aut Kai Ye verfasserin aut Li Guo verfasserin aut Han Xia verfasserin aut Yuanlin Guan verfasserin aut Limin Chai verfasserin aut Wenhua Shi verfasserin aut Cui Zhai verfasserin aut Jian Wang verfasserin aut Xin Yan verfasserin aut Qingting Wang verfasserin aut Qianqian Zhang verfasserin aut Cong Li verfasserin aut Pengtao Liu verfasserin aut Manxiang Li verfasserin aut In Frontiers in Cellular and Infection Microbiology Frontiers Media S.A., 2016 11(2021) (DE-627)664968554 (DE-600)2619676-1 22352988 nnns volume:11 year:2021 https://doi.org/10.3389/fcimb.2021.541092 kostenfrei https://doaj.org/article/7a2ca6c4c27c447da37de9028771fe95 kostenfrei https://www.frontiersin.org/articles/10.3389/fcimb.2021.541092/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 11 2021
language	English
source	In Frontiers in Cellular and Infection Microbiology 11(2021) volume:11 year:2021
sourceStr	In Frontiers in Cellular and Infection Microbiology 11(2021) volume:11 year:2021
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	metagenomic next-generation sequencing (mNGS) bronchoalveolar lavage fluid (BALF) pulmonary infection etiological culture diagnostic Microbiology
isfreeaccess_bool	true
container_title	Frontiers in Cellular and Infection Microbiology
authorswithroles_txt_mv	Yuqian Chen @@aut@@ Wei Feng @@aut@@ Kai Ye @@aut@@ Li Guo @@aut@@ Han Xia @@aut@@ Yuanlin Guan @@aut@@ Limin Chai @@aut@@ Wenhua Shi @@aut@@ Cui Zhai @@aut@@ Jian Wang @@aut@@ Xin Yan @@aut@@ Qingting Wang @@aut@@ Qianqian Zhang @@aut@@ Cong Li @@aut@@ Pengtao Liu @@aut@@ Manxiang Li @@aut@@
publishDateDaySort_date	2021-01-01T00:00:00Z
hierarchy_top_id	664968554
id	DOAJ049713019
language_de	englisch
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callnumber-first	Q - Science
author	Yuqian Chen
spellingShingle	Yuqian Chen misc QR1-502 misc metagenomic next-generation sequencing (mNGS) misc bronchoalveolar lavage fluid (BALF) misc pulmonary infection misc etiological culture misc diagnostic misc Microbiology Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infectious Pathogens From Bronchoalveolar Lavage Samples
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topic_title	QR1-502 Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infectious Pathogens From Bronchoalveolar Lavage Samples metagenomic next-generation sequencing (mNGS) bronchoalveolar lavage fluid (BALF) pulmonary infection etiological culture diagnostic
topic	misc QR1-502 misc metagenomic next-generation sequencing (mNGS) misc bronchoalveolar lavage fluid (BALF) misc pulmonary infection misc etiological culture misc diagnostic misc Microbiology
topic_unstemmed	misc QR1-502 misc metagenomic next-generation sequencing (mNGS) misc bronchoalveolar lavage fluid (BALF) misc pulmonary infection misc etiological culture misc diagnostic misc Microbiology
topic_browse	misc QR1-502 misc metagenomic next-generation sequencing (mNGS) misc bronchoalveolar lavage fluid (BALF) misc pulmonary infection misc etiological culture misc diagnostic misc Microbiology
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title	Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infectious Pathogens From Bronchoalveolar Lavage Samples
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title_full	Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infectious Pathogens From Bronchoalveolar Lavage Samples
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journal	Frontiers in Cellular and Infection Microbiology
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author_browse	Yuqian Chen Wei Feng Kai Ye Li Guo Han Xia Yuanlin Guan Limin Chai Wenhua Shi Cui Zhai Jian Wang Xin Yan Qingting Wang Qianqian Zhang Cong Li Pengtao Liu Manxiang Li
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doi_str_mv	10.3389/fcimb.2021.541092
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title_sort	application of metagenomic next-generation sequencing in the diagnosis of pulmonary infectious pathogens from bronchoalveolar lavage samples
callnumber	QR1-502
title_auth	Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infectious Pathogens From Bronchoalveolar Lavage Samples
abstract	BackgroundMetagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection. In this study, we assessed the value of mNGS for bronchoalveolar lavage (BAL) samples in the diagnosis of pulmonary infections.MethodsFrom February 2018 to April 2019, BAL samples were collected from 235 patients with suspected pulmonary infections. mNGS and microbial culture were performed to evaluate the effectiveness of mNGS in pulmonary infection diagnosis.ResultsWe employed mNGS to evaluate the alpha diversity, results suggesting that patients with confirmed pathogens had a lower microbial diversity index compared to that of patients with uncertain pathogens. For the patients admitted to the respiratory intensive care unit (RICU) or on a ventilator, they experienced a lower diversity index than that of the patients in the general ward or not on a ventilator. In addition, mNGS of BAL had a diagnostic sensitivity of 88.89% and a specificity of 14.86% in pulmonary infection, with 21.16% positive predictive value (PPV) and 83.87% negative predictive value (NPV). When rare pathogens were excluded, the sensitivity of mNGS decreased to 73.33%, and the specificity increased to 41.71%. For patients in the simple pulmonary infection group and the immunocompromised group, the main infection types were bacterial infection (58.33%) and mixed-infection (43.18%). Furthermore, mNGS had an advantage over culture in describing polymicrobial ecosystem, demonstrating the microbial distribution and the dominant strains of the respiratory tract in patients with different underlying diseases.ConclusionsThe study indicated that mNGS of BAL samples could provide more accurate diagnostic information in pulmonary infections and demonstrate the changes of respiratory microbiome in different underlying diseases. This method might play an important role in the clinical use of antimicrobial agents in the future.
abstractGer	BackgroundMetagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection. In this study, we assessed the value of mNGS for bronchoalveolar lavage (BAL) samples in the diagnosis of pulmonary infections.MethodsFrom February 2018 to April 2019, BAL samples were collected from 235 patients with suspected pulmonary infections. mNGS and microbial culture were performed to evaluate the effectiveness of mNGS in pulmonary infection diagnosis.ResultsWe employed mNGS to evaluate the alpha diversity, results suggesting that patients with confirmed pathogens had a lower microbial diversity index compared to that of patients with uncertain pathogens. For the patients admitted to the respiratory intensive care unit (RICU) or on a ventilator, they experienced a lower diversity index than that of the patients in the general ward or not on a ventilator. In addition, mNGS of BAL had a diagnostic sensitivity of 88.89% and a specificity of 14.86% in pulmonary infection, with 21.16% positive predictive value (PPV) and 83.87% negative predictive value (NPV). When rare pathogens were excluded, the sensitivity of mNGS decreased to 73.33%, and the specificity increased to 41.71%. For patients in the simple pulmonary infection group and the immunocompromised group, the main infection types were bacterial infection (58.33%) and mixed-infection (43.18%). Furthermore, mNGS had an advantage over culture in describing polymicrobial ecosystem, demonstrating the microbial distribution and the dominant strains of the respiratory tract in patients with different underlying diseases.ConclusionsThe study indicated that mNGS of BAL samples could provide more accurate diagnostic information in pulmonary infections and demonstrate the changes of respiratory microbiome in different underlying diseases. This method might play an important role in the clinical use of antimicrobial agents in the future.
abstract_unstemmed	BackgroundMetagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection. In this study, we assessed the value of mNGS for bronchoalveolar lavage (BAL) samples in the diagnosis of pulmonary infections.MethodsFrom February 2018 to April 2019, BAL samples were collected from 235 patients with suspected pulmonary infections. mNGS and microbial culture were performed to evaluate the effectiveness of mNGS in pulmonary infection diagnosis.ResultsWe employed mNGS to evaluate the alpha diversity, results suggesting that patients with confirmed pathogens had a lower microbial diversity index compared to that of patients with uncertain pathogens. For the patients admitted to the respiratory intensive care unit (RICU) or on a ventilator, they experienced a lower diversity index than that of the patients in the general ward or not on a ventilator. In addition, mNGS of BAL had a diagnostic sensitivity of 88.89% and a specificity of 14.86% in pulmonary infection, with 21.16% positive predictive value (PPV) and 83.87% negative predictive value (NPV). When rare pathogens were excluded, the sensitivity of mNGS decreased to 73.33%, and the specificity increased to 41.71%. For patients in the simple pulmonary infection group and the immunocompromised group, the main infection types were bacterial infection (58.33%) and mixed-infection (43.18%). Furthermore, mNGS had an advantage over culture in describing polymicrobial ecosystem, demonstrating the microbial distribution and the dominant strains of the respiratory tract in patients with different underlying diseases.ConclusionsThe study indicated that mNGS of BAL samples could provide more accurate diagnostic information in pulmonary infections and demonstrate the changes of respiratory microbiome in different underlying diseases. This method might play an important role in the clinical use of antimicrobial agents in the future.
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title_short	Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infectious Pathogens From Bronchoalveolar Lavage Samples
url	https://doi.org/10.3389/fcimb.2021.541092 https://doaj.org/article/7a2ca6c4c27c447da37de9028771fe95 https://www.frontiersin.org/articles/10.3389/fcimb.2021.541092/full https://doaj.org/toc/2235-2988
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author2	Wei Feng Kai Ye Li Guo Han Xia Yuanlin Guan Limin Chai Wenhua Shi Cui Zhai Jian Wang Xin Yan Qingting Wang Qianqian Zhang Cong Li Pengtao Liu Manxiang Li
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Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infectious Pathogens From Bronchoalveolar Lavage Samples

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