A Microbial World: Could Metagenomic Next-Generation Sequencing Be Involved in Acute Respiratory Failure?
BackgroundThe usefulness of metagenomic next-generation sequencing (mNGS) in identifying pathogens is being investigated. We aimed to compare the power of microbial identification between mNGS and various methods in patients with acute respiratory failure.MethodsWe reviewed 130 patients with respira...
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Frontiers Media S.A.
2021-10-01
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Article |
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English |
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Article |
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DOAJ |
author |
Chunrong Huang Chunrong Huang Chunrong Huang Hong Chen Hong Chen Hong Chen Yongjie Ding Yongjie Ding Yongjie Ding Xiaolong Ma Haixing Zhu Haixing Zhu Haixing Zhu Shengxiong Zhang Shengxiong Zhang Shengxiong Zhang Wei Du Wei Du Wei Du Hanssa Dwarka Summah Guochao Shi Guochao Shi Guochao Shi Yun Feng Yun Feng Yun Feng |
spellingShingle |
Chunrong Huang Chunrong Huang Chunrong Huang Hong Chen Hong Chen Hong Chen Yongjie Ding Yongjie Ding Yongjie Ding Xiaolong Ma Haixing Zhu Haixing Zhu Haixing Zhu Shengxiong Zhang Shengxiong Zhang Shengxiong Zhang Wei Du Wei Du Wei Du Hanssa Dwarka Summah Guochao Shi Guochao Shi Guochao Shi Yun Feng Yun Feng Yun Feng A Microbial World: Could Metagenomic Next-Generation Sequencing Be Involved in Acute Respiratory Failure? Frontiers in Cellular and Infection Microbiology mNGS acute respiratory failure conventional methods microbial detection ptNGS |
author_facet |
Chunrong Huang Chunrong Huang Chunrong Huang Hong Chen Hong Chen Hong Chen Yongjie Ding Yongjie Ding Yongjie Ding Xiaolong Ma Haixing Zhu Haixing Zhu Haixing Zhu Shengxiong Zhang Shengxiong Zhang Shengxiong Zhang Wei Du Wei Du Wei Du Hanssa Dwarka Summah Guochao Shi Guochao Shi Guochao Shi Yun Feng Yun Feng Yun Feng |
author_sort |
Chunrong Huang |
title |
A Microbial World: Could Metagenomic Next-Generation Sequencing Be Involved in Acute Respiratory Failure? |
title_short |
A Microbial World: Could Metagenomic Next-Generation Sequencing Be Involved in Acute Respiratory Failure? |
title_full |
A Microbial World: Could Metagenomic Next-Generation Sequencing Be Involved in Acute Respiratory Failure? |
title_fullStr |
A Microbial World: Could Metagenomic Next-Generation Sequencing Be Involved in Acute Respiratory Failure? |
title_full_unstemmed |
A Microbial World: Could Metagenomic Next-Generation Sequencing Be Involved in Acute Respiratory Failure? |
title_sort |
microbial world: could metagenomic next-generation sequencing be involved in acute respiratory failure? |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Cellular and Infection Microbiology |
issn |
2235-2988 |
publishDate |
2021-10-01 |
description |
BackgroundThe usefulness of metagenomic next-generation sequencing (mNGS) in identifying pathogens is being investigated. We aimed to compare the power of microbial identification between mNGS and various methods in patients with acute respiratory failure.MethodsWe reviewed 130 patients with respiratory failure, and 184 specimens including blood, bronchoalveolar lavage fluid (BALF), sputum, pleural effusion, ascitic fluid, and urine were tested by mNGS and conventional methods (culture, PCR). We also enrolled 13 patients to evaluate the power of mNGS and pathogen targets NGS (ptNGS) in microbial identifications. Clinical features and microbes detected were analyzed.ResultsmNGS outperformed the conventional method in the positive detection rate of Mycobacterium tuberculosis (MTB) (OR, ∞; 95% CI, 1–∞; P < 0.05), bacteria (OR, 3.7; 95% CI, 2.4–5.8; P < 0.0001), fungi (OR, 4.37; 95% CI, 2.7–7.2; P < 0.0001), mycoplasma (OR, 10.5; 95% CI, 31.8–115; P = 0.005), and virus (OR, ∞; 95% CI, 180.7–∞; P < 0.0001). We showed that 20 patients (28 samples) were detected with Pneumocystis jirovecii (P. jirovecii) by mNGS, but not by the conventional method, and most of those patients were immunocompromised. Read numbers of Klebsiella pneumoniae (K. pneumoniae), Acinetobacter baumannii (A. baumannii), Pseudomonas aeruginosa (P. aeruginosa), P. jirovecii, cytomegalovirus (CMV), and Herpes simplex virus 1 (HSV1) in BALF were higher than those in other sample types, and the read number of Candida albicans (C. albicans) in blood was higher than that in BALF. We found that orotracheal intubation and type 2 diabetes mellitus (T2DM) were associated with a higher detection rate of bacteria and virus by mNGS, immunosuppression was associated with a higher detection rate of fungi and virus by mNGS, and inflammatory markers were associated with mNGS-positive detection rate of bacteria. In addition, we observed preliminary results of ptNGS.ConclusionmNGS outperformed the conventional method in the detection of MTB, bacteria, fungi, mycoplasma, and virus. Orotracheal intubation, T2DM, immunosuppression, and inflammatory markers were associated with a higher detection rate of bacteria, fungi, and virus by mNGS. In addition, ptNGS results were consistent with the detection of abundant bacteria, fungi, and mycoplasma in our specimens. |
topic |
mNGS acute respiratory failure conventional methods microbial detection ptNGS |
url |
https://www.frontiersin.org/articles/10.3389/fcimb.2021.738074/full |
work_keys_str_mv |
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doaj-109eebe383df40a5913d0a2170d8f5282021-10-04T14:45:50ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882021-10-011110.3389/fcimb.2021.738074738074A Microbial World: Could Metagenomic Next-Generation Sequencing Be Involved in Acute Respiratory Failure?Chunrong Huang0Chunrong Huang1Chunrong Huang2Hong Chen3Hong Chen4Hong Chen5Yongjie Ding6Yongjie Ding7Yongjie Ding8Xiaolong Ma9Haixing Zhu10Haixing Zhu11Haixing Zhu12Shengxiong Zhang13Shengxiong Zhang14Shengxiong Zhang15Wei Du16Wei Du17Wei Du18Hanssa Dwarka Summah19Guochao Shi20Guochao Shi21Guochao Shi22Yun Feng23Yun Feng24Yun Feng25Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaInstitute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaShanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, ChinaDepartment of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaInstitute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaShanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, ChinaDepartment of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaInstitute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaShanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, ChinaDepartment of Respiratory and Critical Care Medicine, The First Hospital of Jiaxing, Jiaxing, ChinaDepartment of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaInstitute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaShanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, ChinaDepartment of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaInstitute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaShanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, ChinaDepartment of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaInstitute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaShanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, ChinaDepartment of Respiratory and Critical Care Medicine, Poudre D’Or Chest Hospital, Rivière du Rempart, MauritiusDepartment of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaInstitute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaShanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, ChinaDepartment of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaInstitute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaShanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, ChinaBackgroundThe usefulness of metagenomic next-generation sequencing (mNGS) in identifying pathogens is being investigated. We aimed to compare the power of microbial identification between mNGS and various methods in patients with acute respiratory failure.MethodsWe reviewed 130 patients with respiratory failure, and 184 specimens including blood, bronchoalveolar lavage fluid (BALF), sputum, pleural effusion, ascitic fluid, and urine were tested by mNGS and conventional methods (culture, PCR). We also enrolled 13 patients to evaluate the power of mNGS and pathogen targets NGS (ptNGS) in microbial identifications. Clinical features and microbes detected were analyzed.ResultsmNGS outperformed the conventional method in the positive detection rate of Mycobacterium tuberculosis (MTB) (OR, ∞; 95% CI, 1–∞; P < 0.05), bacteria (OR, 3.7; 95% CI, 2.4–5.8; P < 0.0001), fungi (OR, 4.37; 95% CI, 2.7–7.2; P < 0.0001), mycoplasma (OR, 10.5; 95% CI, 31.8–115; P = 0.005), and virus (OR, ∞; 95% CI, 180.7–∞; P < 0.0001). We showed that 20 patients (28 samples) were detected with Pneumocystis jirovecii (P. jirovecii) by mNGS, but not by the conventional method, and most of those patients were immunocompromised. Read numbers of Klebsiella pneumoniae (K. pneumoniae), Acinetobacter baumannii (A. baumannii), Pseudomonas aeruginosa (P. aeruginosa), P. jirovecii, cytomegalovirus (CMV), and Herpes simplex virus 1 (HSV1) in BALF were higher than those in other sample types, and the read number of Candida albicans (C. albicans) in blood was higher than that in BALF. We found that orotracheal intubation and type 2 diabetes mellitus (T2DM) were associated with a higher detection rate of bacteria and virus by mNGS, immunosuppression was associated with a higher detection rate of fungi and virus by mNGS, and inflammatory markers were associated with mNGS-positive detection rate of bacteria. In addition, we observed preliminary results of ptNGS.ConclusionmNGS outperformed the conventional method in the detection of MTB, bacteria, fungi, mycoplasma, and virus. Orotracheal intubation, T2DM, immunosuppression, and inflammatory markers were associated with a higher detection rate of bacteria, fungi, and virus by mNGS. In addition, ptNGS results were consistent with the detection of abundant bacteria, fungi, and mycoplasma in our specimens.https://www.frontiersin.org/articles/10.3389/fcimb.2021.738074/fullmNGSacute respiratory failureconventional methodsmicrobial detectionptNGS |