Evaluation of Cell-Free DNA-Based Next-Generation Sequencing for Identifying Pathogens in Bacteremia Patients
Rapid detection of bloodstream pathogens would greatly facilitate clinicians to make precise antimicrobial treatment in patients with bacteremia. In this study, 114 plasma samples were collected from patients with identified or suspected bacteremia, and pathogens were detected by the conventional bl...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Sciendo
2022-11-01
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| Series: | Polish Journal of Microbiology |
| Subjects: | |
| Online Access: | https://doi.org/10.33073/pjm-2022-043 |
| _version_ | 1828058679500341248 |
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| author | Zhang Chaoqin Cheng Hang Zhao Yuxi Chen Jinlian Li Meng Yu Zhijian Sun Xiang Li Peiyu Shang Yongpeng Ma Jinmin Zheng Jinxin |
| author_facet | Zhang Chaoqin Cheng Hang Zhao Yuxi Chen Jinlian Li Meng Yu Zhijian Sun Xiang Li Peiyu Shang Yongpeng Ma Jinmin Zheng Jinxin |
| author_sort | Zhang Chaoqin |
| collection | DOAJ |
| description | Rapid detection of bloodstream pathogens would greatly facilitate clinicians to make precise antimicrobial treatment in patients with bacteremia. In this study, 114 plasma samples were collected from patients with identified or suspected bacteremia, and pathogens were detected by the conventional blood culture (BC) and cell-free DNA metagenomics next-generation sequencing (cfDNA mNGS). The present study indicated that 76% (38/50) of positive conventional blood culture (BC+ group) patients were positively detected by cfDNA mNGS, and only 4% were mismatched between cfDNA mNGS and conventional bacteria culture. Pathogens in 32.8% of suspected bacteremia patients with negative conventional blood culture (BC– group) were determined accurately by cfDNA mNGS combined with analyzing the patients’ clinical manifestations. Escherichia coli and Klebsiella pneumoniae were the most detected pathogens in identified bacteremia patients by cfDNA mNGS. 76.2% (16/21) of E. coli and 92.3% (12/13) of K. pneumoniae in bacteremia patients were identified by conventional blood cultures that were also detected by cfDNA mNGS. This study demonstrated that genomic coverage of E. coli and K. pneumoniae were more often detected in BC+ group patients and genomic coverage of Acinetobacter johnsonii and Paucibacter sp. KCTC 42545 was more often detected in BC– group patients. In conclusion, cfDNA mNGS could rapidly and precisely provide an alternative detection method for the diagnosis of bacteremia. |
| first_indexed | 2024-04-10T21:31:32Z |
| format | Article |
| id | doaj.art-3b77d8fa7fa443fcadf505288dcef215 |
| institution | Directory Open Access Journal |
| issn | 2544-4646 |
| language | English |
| last_indexed | 2024-04-10T21:31:32Z |
| publishDate | 2022-11-01 |
| publisher | Sciendo |
| record_format | Article |
| series | Polish Journal of Microbiology |
| spelling | doaj.art-3b77d8fa7fa443fcadf505288dcef2152023-01-19T13:20:30ZengSciendoPolish Journal of Microbiology2544-46462022-11-0171449950710.33073/pjm-2022-043Evaluation of Cell-Free DNA-Based Next-Generation Sequencing for Identifying Pathogens in Bacteremia PatientsZhang Chaoqin0Cheng Hang1Zhao Yuxi2Chen Jinlian3Li Meng4Yu Zhijian5Sun Xiang6Li Peiyu7Shang Yongpeng8Ma Jinmin9Zheng Jinxin10Department of Infectious Diseases and the Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, ChinaDepartment of Infectious Diseases and the Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, ChinaDepartment of Infectious Diseases and the Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, ChinaDepartment of Infectious Diseases and the Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, ChinaBGI-Shenzhen, Shenzhen, ChinaDepartment of Infectious Diseases and the Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, ChinaDepartment of Infectious Diseases and the Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, ChinaDepartment of Infectious Diseases and the Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, ChinaDepartment of Infectious Diseases and the Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, ChinaBGI-Shenzhen, Shenzhen, ChinaDepartment of Infectious Diseases and the Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, ChinaRapid detection of bloodstream pathogens would greatly facilitate clinicians to make precise antimicrobial treatment in patients with bacteremia. In this study, 114 plasma samples were collected from patients with identified or suspected bacteremia, and pathogens were detected by the conventional blood culture (BC) and cell-free DNA metagenomics next-generation sequencing (cfDNA mNGS). The present study indicated that 76% (38/50) of positive conventional blood culture (BC+ group) patients were positively detected by cfDNA mNGS, and only 4% were mismatched between cfDNA mNGS and conventional bacteria culture. Pathogens in 32.8% of suspected bacteremia patients with negative conventional blood culture (BC– group) were determined accurately by cfDNA mNGS combined with analyzing the patients’ clinical manifestations. Escherichia coli and Klebsiella pneumoniae were the most detected pathogens in identified bacteremia patients by cfDNA mNGS. 76.2% (16/21) of E. coli and 92.3% (12/13) of K. pneumoniae in bacteremia patients were identified by conventional blood cultures that were also detected by cfDNA mNGS. This study demonstrated that genomic coverage of E. coli and K. pneumoniae were more often detected in BC+ group patients and genomic coverage of Acinetobacter johnsonii and Paucibacter sp. KCTC 42545 was more often detected in BC– group patients. In conclusion, cfDNA mNGS could rapidly and precisely provide an alternative detection method for the diagnosis of bacteremia.https://doi.org/10.33073/pjm-2022-043cell-free dnanext-generation sequencingbacteremiablood culturepathogens |
| spellingShingle | Zhang Chaoqin Cheng Hang Zhao Yuxi Chen Jinlian Li Meng Yu Zhijian Sun Xiang Li Peiyu Shang Yongpeng Ma Jinmin Zheng Jinxin Evaluation of Cell-Free DNA-Based Next-Generation Sequencing for Identifying Pathogens in Bacteremia Patients Polish Journal of Microbiology cell-free dna next-generation sequencing bacteremia blood culture pathogens |
| title | Evaluation of Cell-Free DNA-Based Next-Generation Sequencing for Identifying Pathogens in Bacteremia Patients |
| title_full | Evaluation of Cell-Free DNA-Based Next-Generation Sequencing for Identifying Pathogens in Bacteremia Patients |
| title_fullStr | Evaluation of Cell-Free DNA-Based Next-Generation Sequencing for Identifying Pathogens in Bacteremia Patients |
| title_full_unstemmed | Evaluation of Cell-Free DNA-Based Next-Generation Sequencing for Identifying Pathogens in Bacteremia Patients |
| title_short | Evaluation of Cell-Free DNA-Based Next-Generation Sequencing for Identifying Pathogens in Bacteremia Patients |
| title_sort | evaluation of cell free dna based next generation sequencing for identifying pathogens in bacteremia patients |
| topic | cell-free dna next-generation sequencing bacteremia blood culture pathogens |
| url | https://doi.org/10.33073/pjm-2022-043 |
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