Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia
BackgroundCommunity-acquired pneumonia (CAP) is an extraordinarily heterogeneous illness, both in the range of responsible pathogens and the host response. Metagenomic next-generation sequencing (mNGS) is a promising technology for pathogen detection. However, the clinical application of mNGS for pa...
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| Format: | Article |
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2023.1136588/full |
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| author | Tianlai Lin Xueliang Tu Jiangman Zhao Jiangman Zhao Ling Huang Xiaodong Dai Xiaoling Chen Yue Xu Yue Xu Wushuang Li Wushuang Li Yaoyao Wang Yaoyao Wang Jingwei Lou Jingwei Lou Shouxin Wu Hongling Zhang |
| author_facet | Tianlai Lin Xueliang Tu Jiangman Zhao Jiangman Zhao Ling Huang Xiaodong Dai Xiaoling Chen Yue Xu Yue Xu Wushuang Li Wushuang Li Yaoyao Wang Yaoyao Wang Jingwei Lou Jingwei Lou Shouxin Wu Hongling Zhang |
| author_sort | Tianlai Lin |
| collection | DOAJ |
| description | BackgroundCommunity-acquired pneumonia (CAP) is an extraordinarily heterogeneous illness, both in the range of responsible pathogens and the host response. Metagenomic next-generation sequencing (mNGS) is a promising technology for pathogen detection. However, the clinical application of mNGS for pathogen detection remains challenging.MethodsA total of 205 patients with CAP admitted to the intensive care unit were recruited, and broncho alveolar lavage fluids (BALFs) from 83 patients, sputum samples from 33 cases, and blood from 89 cases were collected for pathogen detection by mNGS. At the same time, multiple samples of each patient were tested by culture. The diagnostic performance was compared between mNGS and culture for pathogen detection.ResultsThe positive rate of pathogen detection by mNGS in BALF and sputum samples was 89.2% and 97.0%, which was significantly higher (P < 0.001) than that (67.4%) of blood samples. The positive rate of mNGS was significantly higher than that of culture (81.0% vs. 56.1%, P = 1.052e-07). A group of pathogens including Mycobacterium abscessus, Chlamydia psittaci, Pneumocystis jirovecii, Orientia tsutsugamushi, and all viruses were only detected by mNGS. Based on mNGS results, Escherichia coli was the most common pathogen (15/61, 24.59%) of non-severe patients with CAP, and Mycobacterium tuberculosis was the most common pathogen (21/144, 14.58%) leading to severe pneumonia. Pneumocystis jirovecii was the most common pathogen (26.09%) in severe CAP patients with an immunocompromised status, which was all detected by mNGS only.ConclusionmNGS has higher overall sensitivity for pathogen detection than culture, BALF, and sputum mNGS are more sensitive than blood mNGS. mNGS is a necessary supplement of conventional microbiological tests for the pathogen detection of pulmonary infection. |
| first_indexed | 2024-03-12T14:51:24Z |
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| id | doaj.art-1cfde1b8608c4255832da09c63bfd1a0 |
| institution | Directory Open Access Journal |
| issn | 2235-2988 |
| language | English |
| last_indexed | 2024-03-12T14:51:24Z |
| publishDate | 2023-03-01 |
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| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj.art-1cfde1b8608c4255832da09c63bfd1a02023-08-15T12:43:18ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882023-03-011310.3389/fcimb.2023.11365881136588Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumoniaTianlai Lin0Xueliang Tu1Jiangman Zhao2Jiangman Zhao3Ling Huang4Xiaodong Dai5Xiaoling Chen6Yue Xu7Yue Xu8Wushuang Li9Wushuang Li10Yaoyao Wang11Yaoyao Wang12Jingwei Lou13Jingwei Lou14Shouxin Wu15Hongling Zhang16Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, ChinaDepartment of Clinical Laboratory, Huanghe Sanmenxia Hospital Affiliated to Henan University of Science and Technology, Sanmenxia, ChinaShanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, ChinaShanghai Zhangjiang Institute of Medical Innovation, Shanghai, ChinaDepartment of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, ChinaDepartment of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, ChinaDepartment of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, ChinaShanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, ChinaShanghai Zhangjiang Institute of Medical Innovation, Shanghai, ChinaShanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, ChinaShanghai Zhangjiang Institute of Medical Innovation, Shanghai, ChinaShanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, ChinaShanghai Zhangjiang Institute of Medical Innovation, Shanghai, ChinaShanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, ChinaShanghai Zhangjiang Institute of Medical Innovation, Shanghai, ChinaShanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, ChinaDepartment of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, ChinaBackgroundCommunity-acquired pneumonia (CAP) is an extraordinarily heterogeneous illness, both in the range of responsible pathogens and the host response. Metagenomic next-generation sequencing (mNGS) is a promising technology for pathogen detection. However, the clinical application of mNGS for pathogen detection remains challenging.MethodsA total of 205 patients with CAP admitted to the intensive care unit were recruited, and broncho alveolar lavage fluids (BALFs) from 83 patients, sputum samples from 33 cases, and blood from 89 cases were collected for pathogen detection by mNGS. At the same time, multiple samples of each patient were tested by culture. The diagnostic performance was compared between mNGS and culture for pathogen detection.ResultsThe positive rate of pathogen detection by mNGS in BALF and sputum samples was 89.2% and 97.0%, which was significantly higher (P < 0.001) than that (67.4%) of blood samples. The positive rate of mNGS was significantly higher than that of culture (81.0% vs. 56.1%, P = 1.052e-07). A group of pathogens including Mycobacterium abscessus, Chlamydia psittaci, Pneumocystis jirovecii, Orientia tsutsugamushi, and all viruses were only detected by mNGS. Based on mNGS results, Escherichia coli was the most common pathogen (15/61, 24.59%) of non-severe patients with CAP, and Mycobacterium tuberculosis was the most common pathogen (21/144, 14.58%) leading to severe pneumonia. Pneumocystis jirovecii was the most common pathogen (26.09%) in severe CAP patients with an immunocompromised status, which was all detected by mNGS only.ConclusionmNGS has higher overall sensitivity for pathogen detection than culture, BALF, and sputum mNGS are more sensitive than blood mNGS. mNGS is a necessary supplement of conventional microbiological tests for the pathogen detection of pulmonary infection.https://www.frontiersin.org/articles/10.3389/fcimb.2023.1136588/fullmetagenomic next-generation sequencingculturecommunity-acquired pneumoniaconventional microbiological testpathogen detection |
| spellingShingle | Tianlai Lin Xueliang Tu Jiangman Zhao Jiangman Zhao Ling Huang Xiaodong Dai Xiaoling Chen Yue Xu Yue Xu Wushuang Li Wushuang Li Yaoyao Wang Yaoyao Wang Jingwei Lou Jingwei Lou Shouxin Wu Hongling Zhang Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia Frontiers in Cellular and Infection Microbiology metagenomic next-generation sequencing culture community-acquired pneumonia conventional microbiological test pathogen detection |
| title | Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia |
| title_full | Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia |
| title_fullStr | Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia |
| title_full_unstemmed | Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia |
| title_short | Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia |
| title_sort | microbiological diagnostic performance of metagenomic next generation sequencing compared with conventional culture for patients with community acquired pneumonia |
| topic | metagenomic next-generation sequencing culture community-acquired pneumonia conventional microbiological test pathogen detection |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2023.1136588/full |
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