A Retrospective Paired Comparison Between Untargeted Next Generation Sequencing and Conventional Microbiology Tests With Wisely Chosen Metagenomic Sequencing Positive Criteria
Objectives: To evaluate the performance of metagenomic next generation sequencing (mNGS) using adequate criteria for the detection of pathogens in lower respiratory tract (LRT) samples with a paired comparison to conventional microbiology tests (CMT).Methods: One hundred sixty-seven patients were re...
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Frontiers Media S.A.
2021-10-01
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| Series: | Frontiers in Medicine |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmed.2021.686247/full |
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| author | Hanyu Qin Jinmin Peng Ling Liu Jing Wu Lingai Pan Lingai Pan Xiaobo Huang Xiaobo Huang Man Huang Haibo Qiu Bin Du The China Critical Care Clinical Trials Group (CCCCTG) |
| author_facet | Hanyu Qin Jinmin Peng Ling Liu Jing Wu Lingai Pan Lingai Pan Xiaobo Huang Xiaobo Huang Man Huang Haibo Qiu Bin Du The China Critical Care Clinical Trials Group (CCCCTG) |
| author_sort | Hanyu Qin |
| collection | DOAJ |
| description | Objectives: To evaluate the performance of metagenomic next generation sequencing (mNGS) using adequate criteria for the detection of pathogens in lower respiratory tract (LRT) samples with a paired comparison to conventional microbiology tests (CMT).Methods: One hundred sixty-seven patients were reviewed from four different intensive care units (ICUs) in mainland China during 2018 with both mNGS and CMT results of LRT samples available. The reads per million ratio (RPMsample/RPMnon−template−control ratio) and standardized strictly mapped reads number (SDSMRN) were the two criteria chosen for identifying positive pathogens reported from mNGS. A McNemar test was used for a paired comparison analysis between mNGS and CMT.Results: One hundred forty-nine cases were counted into the final analysis. The RPMsample/RPMNTC ratio criterion performed better with a higher accuracy for bacteria, fungi, and virus than SDSMRN criterion [bacteria (RPMsample/RPMNTC ratio vs. SDSMRN), 65.1 vs. 55.7%; fungi, 75.8 vs. 71.1%; DNA virus, 86.3 vs. 74.5%; RNA virus, 90.9 vs. 81.8%]. The mNGS was also superior in bacteria detection only if an SDSMRN ≥3 was used as a positive criterion with a paired comparison to culture [SDSMRN positive, 92/149 (61.7%); culture positive, 54/149 (36.2%); p < 0.001]; however, it was outperformed with significantly more fungi and DNA virus identification when choosing both criteria for positive outliers [fungi (RPMsample/RPMNTC ratio vs. SDSMRN vs. culture), 23.5 vs. 29.5 vs. 8.7%, p < 0.001; DNA virus (RPMsample/RPMNTC ratio vs. SDSMRN vs. PCR), 14.1 vs. 20.8 vs. 11.8%, p < 0.05].Conclusions: Metagenomic next generation sequencing may contribute to revealing the LRT infection etiology in hospitalized groups of potential fungal infections and in situations with less access to the multiplex PCR of LRT samples from the laboratory by choosing a wise criterion like the RPMsample/RPMNTC ratio. |
| first_indexed | 2024-12-19T22:53:49Z |
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| id | doaj.art-7c4182a4e0964b4988f3a7bc52cca1a8 |
| institution | Directory Open Access Journal |
| issn | 2296-858X |
| language | English |
| last_indexed | 2024-12-19T22:53:49Z |
| publishDate | 2021-10-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Medicine |
| spelling | doaj.art-7c4182a4e0964b4988f3a7bc52cca1a82022-12-21T20:02:42ZengFrontiers Media S.A.Frontiers in Medicine2296-858X2021-10-01810.3389/fmed.2021.686247686247A Retrospective Paired Comparison Between Untargeted Next Generation Sequencing and Conventional Microbiology Tests With Wisely Chosen Metagenomic Sequencing Positive CriteriaHanyu Qin0Jinmin Peng1Ling Liu2Jing Wu3Lingai Pan4Lingai Pan5Xiaobo Huang6Xiaobo Huang7Man Huang8Haibo Qiu9Bin Du10The China Critical Care Clinical Trials Group (CCCCTG)11State Key Laboratory of Complex, Severe and Rare Disease, Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, ChinaState Key Laboratory of Complex, Severe and Rare Disease, Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, ChinaDepartment of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, ChinaDepartment of Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ChinaDepartment of Critical Care Medicine, Sichuan Provincial Hospital, University of Electronic Science and Technology of China, Chengdu, ChinaSichuan Translational Medicine Research Hospital, Chinese Academy of Sciences, Chengdu, ChinaDepartment of Critical Care Medicine, Sichuan Provincial Hospital, University of Electronic Science and Technology of China, Chengdu, ChinaSichuan Translational Medicine Research Hospital, Chinese Academy of Sciences, Chengdu, ChinaDepartment of Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ChinaDepartment of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, ChinaState Key Laboratory of Complex, Severe and Rare Disease, Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, ChinaState Key Laboratory of Complex, Severe and Rare Disease, Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, ChinaObjectives: To evaluate the performance of metagenomic next generation sequencing (mNGS) using adequate criteria for the detection of pathogens in lower respiratory tract (LRT) samples with a paired comparison to conventional microbiology tests (CMT).Methods: One hundred sixty-seven patients were reviewed from four different intensive care units (ICUs) in mainland China during 2018 with both mNGS and CMT results of LRT samples available. The reads per million ratio (RPMsample/RPMnon−template−control ratio) and standardized strictly mapped reads number (SDSMRN) were the two criteria chosen for identifying positive pathogens reported from mNGS. A McNemar test was used for a paired comparison analysis between mNGS and CMT.Results: One hundred forty-nine cases were counted into the final analysis. The RPMsample/RPMNTC ratio criterion performed better with a higher accuracy for bacteria, fungi, and virus than SDSMRN criterion [bacteria (RPMsample/RPMNTC ratio vs. SDSMRN), 65.1 vs. 55.7%; fungi, 75.8 vs. 71.1%; DNA virus, 86.3 vs. 74.5%; RNA virus, 90.9 vs. 81.8%]. The mNGS was also superior in bacteria detection only if an SDSMRN ≥3 was used as a positive criterion with a paired comparison to culture [SDSMRN positive, 92/149 (61.7%); culture positive, 54/149 (36.2%); p < 0.001]; however, it was outperformed with significantly more fungi and DNA virus identification when choosing both criteria for positive outliers [fungi (RPMsample/RPMNTC ratio vs. SDSMRN vs. culture), 23.5 vs. 29.5 vs. 8.7%, p < 0.001; DNA virus (RPMsample/RPMNTC ratio vs. SDSMRN vs. PCR), 14.1 vs. 20.8 vs. 11.8%, p < 0.05].Conclusions: Metagenomic next generation sequencing may contribute to revealing the LRT infection etiology in hospitalized groups of potential fungal infections and in situations with less access to the multiplex PCR of LRT samples from the laboratory by choosing a wise criterion like the RPMsample/RPMNTC ratio.https://www.frontiersin.org/articles/10.3389/fmed.2021.686247/fullmetagenomic sequencingpathogen detectionlower respiratory tract infectionconventional microbiology testspositive criteria |
| spellingShingle | Hanyu Qin Jinmin Peng Ling Liu Jing Wu Lingai Pan Lingai Pan Xiaobo Huang Xiaobo Huang Man Huang Haibo Qiu Bin Du The China Critical Care Clinical Trials Group (CCCCTG) A Retrospective Paired Comparison Between Untargeted Next Generation Sequencing and Conventional Microbiology Tests With Wisely Chosen Metagenomic Sequencing Positive Criteria Frontiers in Medicine metagenomic sequencing pathogen detection lower respiratory tract infection conventional microbiology tests positive criteria |
| title | A Retrospective Paired Comparison Between Untargeted Next Generation Sequencing and Conventional Microbiology Tests With Wisely Chosen Metagenomic Sequencing Positive Criteria |
| title_full | A Retrospective Paired Comparison Between Untargeted Next Generation Sequencing and Conventional Microbiology Tests With Wisely Chosen Metagenomic Sequencing Positive Criteria |
| title_fullStr | A Retrospective Paired Comparison Between Untargeted Next Generation Sequencing and Conventional Microbiology Tests With Wisely Chosen Metagenomic Sequencing Positive Criteria |
| title_full_unstemmed | A Retrospective Paired Comparison Between Untargeted Next Generation Sequencing and Conventional Microbiology Tests With Wisely Chosen Metagenomic Sequencing Positive Criteria |
| title_short | A Retrospective Paired Comparison Between Untargeted Next Generation Sequencing and Conventional Microbiology Tests With Wisely Chosen Metagenomic Sequencing Positive Criteria |
| title_sort | retrospective paired comparison between untargeted next generation sequencing and conventional microbiology tests with wisely chosen metagenomic sequencing positive criteria |
| topic | metagenomic sequencing pathogen detection lower respiratory tract infection conventional microbiology tests positive criteria |
| url | https://www.frontiersin.org/articles/10.3389/fmed.2021.686247/full |
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