Detection of pathogens from resected heart valves of patients with infective endocarditis by next-generation sequencing
Objectives: Identification of the underlying pathogens of infective endocarditis (IE) is critical for precision therapy. Methods: We evaluated a metagenomic method with next-generation sequencing (NGS) for the direct detection of pathogens from the resected valves of 44 IE patients and seven rejecte...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2019-06-01
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| Series: | International Journal of Infectious Diseases |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1201971219301341 |
| _version_ | 1818521687462772736 |
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| author | Jun Cheng Huan Hu Wei Fang Duozhi Shi Chen Liang Yang Sun GuoFeng Gao Hao Wang Qian Zhang LiQing Wang HongLong Wu Long Hu Luyao Chen Jin Zhang Shela Lee FeiYan Wang Zhou Zhou |
| author_facet | Jun Cheng Huan Hu Wei Fang Duozhi Shi Chen Liang Yang Sun GuoFeng Gao Hao Wang Qian Zhang LiQing Wang HongLong Wu Long Hu Luyao Chen Jin Zhang Shela Lee FeiYan Wang Zhou Zhou |
| author_sort | Jun Cheng |
| collection | DOAJ |
| description | Objectives: Identification of the underlying pathogens of infective endocarditis (IE) is critical for precision therapy. Methods: We evaluated a metagenomic method with next-generation sequencing (NGS) for the direct detection of pathogens from the resected valves of 44 IE patients and seven rejected IE patients according to the modified Duke criteria. Results: NGS displayed sensitivity, specificity, positive predictive values and negative predictive values of 97.6%, 85.7%, 97.6%, and 85.7% compared with 46.2%, 100%, 100%, and 12.5% for blood culture and 17.1%, 100%, 100%, and 17.1% for valve culture and 51.4%, 100%, 100%, and 26.1% for valve Gram staining, respectively. Conclusions: NGS technique had superior sensitivity and shorter turnaround time compared with culture-based methods for identifying causative pathogens of IE. The NGS technology should be considered an essential supplement to culture-based methods, particularly for unculturable or difficult-to-culture microorganisms. Keywords: Metagenomics shotgun, Next-generation sequencing, Infective endocarditis, Diagnosis |
| first_indexed | 2024-12-11T01:54:45Z |
| format | Article |
| id | doaj.art-4f48c9b93664456fbe15208240fa895c |
| institution | Directory Open Access Journal |
| issn | 1201-9712 |
| language | English |
| last_indexed | 2024-12-11T01:54:45Z |
| publishDate | 2019-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | International Journal of Infectious Diseases |
| spelling | doaj.art-4f48c9b93664456fbe15208240fa895c2022-12-22T01:24:40ZengElsevierInternational Journal of Infectious Diseases1201-97122019-06-0183148153Detection of pathogens from resected heart valves of patients with infective endocarditis by next-generation sequencingJun Cheng0Huan Hu1Wei Fang2Duozhi Shi3Chen Liang4Yang Sun5GuoFeng Gao6Hao Wang7Qian Zhang8LiQing Wang9HongLong Wu10Long Hu11Luyao Chen12Jin Zhang13Shela Lee14FeiYan Wang15Zhou Zhou16State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, ChinaState Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China; State Key Laboratory of Translational Medicine and Innovative Drug Development, Simcere Diagnostics Co., Ltd., Nanjing 210042, ChinaState Key Laboratory of Translational Medicine and Innovative Drug Development, Simcere Diagnostics Co., Ltd., Nanjing 210042, ChinaState Key Laboratory of Translational Medicine and Innovative Drug Development, Simcere Diagnostics Co., Ltd., Nanjing 210042, ChinaState Key Laboratory of Translational Medicine and Innovative Drug Development, Simcere Diagnostics Co., Ltd., Nanjing 210042, ChinaState Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, ChinaDepartment of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100037, ChinaDepartment of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100037, ChinaDepartment of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100037, ChinaCenter of Cardiac Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, ChinaBinhai Genomics Institute, Tianjin Translational Genomics Center, BGI-Tianjin BGI-Shenzhen, Tianjin 300308, ChinaState Key Laboratory of Translational Medicine and Innovative Drug Development, Simcere Diagnostics Co., Ltd., Nanjing 210042, ChinaState Key Laboratory of Translational Medicine and Innovative Drug Development, Simcere Diagnostics Co., Ltd., Nanjing 210042, ChinaState Key Laboratory of Translational Medicine and Innovative Drug Development, Simcere Diagnostics Co., Ltd., Nanjing 210042, ChinaState Key Laboratory of Translational Medicine and Innovative Drug Development, Simcere Diagnostics Co., Ltd., Nanjing 210042, China; Corresponding authors.State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China; Corresponding authors.State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China; Corresponding authors.Objectives: Identification of the underlying pathogens of infective endocarditis (IE) is critical for precision therapy. Methods: We evaluated a metagenomic method with next-generation sequencing (NGS) for the direct detection of pathogens from the resected valves of 44 IE patients and seven rejected IE patients according to the modified Duke criteria. Results: NGS displayed sensitivity, specificity, positive predictive values and negative predictive values of 97.6%, 85.7%, 97.6%, and 85.7% compared with 46.2%, 100%, 100%, and 12.5% for blood culture and 17.1%, 100%, 100%, and 17.1% for valve culture and 51.4%, 100%, 100%, and 26.1% for valve Gram staining, respectively. Conclusions: NGS technique had superior sensitivity and shorter turnaround time compared with culture-based methods for identifying causative pathogens of IE. The NGS technology should be considered an essential supplement to culture-based methods, particularly for unculturable or difficult-to-culture microorganisms. Keywords: Metagenomics shotgun, Next-generation sequencing, Infective endocarditis, Diagnosishttp://www.sciencedirect.com/science/article/pii/S1201971219301341 |
| spellingShingle | Jun Cheng Huan Hu Wei Fang Duozhi Shi Chen Liang Yang Sun GuoFeng Gao Hao Wang Qian Zhang LiQing Wang HongLong Wu Long Hu Luyao Chen Jin Zhang Shela Lee FeiYan Wang Zhou Zhou Detection of pathogens from resected heart valves of patients with infective endocarditis by next-generation sequencing International Journal of Infectious Diseases |
| title | Detection of pathogens from resected heart valves of patients with infective endocarditis by next-generation sequencing |
| title_full | Detection of pathogens from resected heart valves of patients with infective endocarditis by next-generation sequencing |
| title_fullStr | Detection of pathogens from resected heart valves of patients with infective endocarditis by next-generation sequencing |
| title_full_unstemmed | Detection of pathogens from resected heart valves of patients with infective endocarditis by next-generation sequencing |
| title_short | Detection of pathogens from resected heart valves of patients with infective endocarditis by next-generation sequencing |
| title_sort | detection of pathogens from resected heart valves of patients with infective endocarditis by next generation sequencing |
| url | http://www.sciencedirect.com/science/article/pii/S1201971219301341 |
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