Clinical evaluation of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community-acquired pneumonia
This study is to evaluate the usefulness of pathogen detection using metagenomic next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) specimens from children with community-acquired pneumonia (CAP). We retrospectively collected BALF specimens from 121 children with CAP at Tianjin...
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Frontiers Media S.A.
2022-07-01
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| Series: | Frontiers in Medicine |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmed.2022.952636/full |
| _version_ | 1828759718544277504 |
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| author | Wei Guo Wei Guo Xiaojian Cui Qiushi Wang Yupeng Wei Yanqing Guo Tongqiang Zhang Tongqiang Zhang Jianghua Zhan Jianghua Zhan |
| author_facet | Wei Guo Wei Guo Xiaojian Cui Qiushi Wang Yupeng Wei Yanqing Guo Tongqiang Zhang Tongqiang Zhang Jianghua Zhan Jianghua Zhan |
| author_sort | Wei Guo |
| collection | DOAJ |
| description | This study is to evaluate the usefulness of pathogen detection using metagenomic next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) specimens from children with community-acquired pneumonia (CAP). We retrospectively collected BALF specimens from 121 children with CAP at Tianjin Children's Hospital from February 2021 to December 2021. The diagnostic performances of mNGS and conventional tests (CT) (culture and targeted polymerase chain reaction tests) were compared, using composite diagnosis as the reference standard. The results of mNGS and CT were compared based on pathogenic and non-pathogenic organisms. Pathogen profiles and co-infections between the mild CAP and severe CAP groups were also analyzed. The overall positive coincidence rate was 86.78% (105/121) for mNGS and 66.94% (81/121) for CT. The proportion of patients diagnosed using mNGS plus CT increased to 99.18%. Among the patients, 17.36% were confirmed only by mNGS; Streptococcus pneumoniae accounted for 52.38% and 23.8% of the patients were co-infected. Moreover, Bordetella pertussis and Human bocavirus (HBoV) were detected only using mNGS. Mycoplasma pneumoniae, which was identified in 89 (73.55%) of 121 children with CAP, was the most frequent pathogen detected using mNGS. The infection rate of M. pneumoniae in the severe CAP group was significantly higher than that in the mild CAP group (P = 0.007). The symptoms of single bacterial infections (except for mycoplasma) were milder than those of mycoplasma infections. mNGS identified more bacterial infections when compared to the CT methods and was able to identify co-infections which were initially missed on CT. Additionally, it was able to identify pathogens that were beyond the scope of the CT methods. The mNGS method is a powerful supplement to clinical diagnostic tools in respiratory infections, as it can increase the precision of diagnosis and guide the use of antibiotics. |
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| id | doaj.art-3e76ab3c5b4d412eb96ccb0fa8ebf688 |
| institution | Directory Open Access Journal |
| issn | 2296-858X |
| language | English |
| last_indexed | 2024-12-11T01:01:40Z |
| publishDate | 2022-07-01 |
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| spelling | doaj.art-3e76ab3c5b4d412eb96ccb0fa8ebf6882022-12-22T01:26:18ZengFrontiers Media S.A.Frontiers in Medicine2296-858X2022-07-01910.3389/fmed.2022.952636952636Clinical evaluation of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community-acquired pneumoniaWei Guo0Wei Guo1Xiaojian Cui2Qiushi Wang3Yupeng Wei4Yanqing Guo5Tongqiang Zhang6Tongqiang Zhang7Jianghua Zhan8Jianghua Zhan9Clinical School of Paediatrics, Tianjin Medical University, Tianjin, ChinaDepartment of Respiratory Medicine, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, ChinaDepartment of Clinical Lab, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, ChinaInfection Business Unit, Tianjin Novogene Med LAB Co., Ltd., Tianjin, ChinaDepartment of Respiratory Medicine, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, ChinaInfection Business Unit, Tianjin Novogene Med LAB Co., Ltd., Tianjin, ChinaClinical School of Paediatrics, Tianjin Medical University, Tianjin, ChinaDepartment of Respiratory Medicine, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, ChinaClinical School of Paediatrics, Tianjin Medical University, Tianjin, ChinaDepartment of Pediatric Surgery, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, ChinaThis study is to evaluate the usefulness of pathogen detection using metagenomic next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) specimens from children with community-acquired pneumonia (CAP). We retrospectively collected BALF specimens from 121 children with CAP at Tianjin Children's Hospital from February 2021 to December 2021. The diagnostic performances of mNGS and conventional tests (CT) (culture and targeted polymerase chain reaction tests) were compared, using composite diagnosis as the reference standard. The results of mNGS and CT were compared based on pathogenic and non-pathogenic organisms. Pathogen profiles and co-infections between the mild CAP and severe CAP groups were also analyzed. The overall positive coincidence rate was 86.78% (105/121) for mNGS and 66.94% (81/121) for CT. The proportion of patients diagnosed using mNGS plus CT increased to 99.18%. Among the patients, 17.36% were confirmed only by mNGS; Streptococcus pneumoniae accounted for 52.38% and 23.8% of the patients were co-infected. Moreover, Bordetella pertussis and Human bocavirus (HBoV) were detected only using mNGS. Mycoplasma pneumoniae, which was identified in 89 (73.55%) of 121 children with CAP, was the most frequent pathogen detected using mNGS. The infection rate of M. pneumoniae in the severe CAP group was significantly higher than that in the mild CAP group (P = 0.007). The symptoms of single bacterial infections (except for mycoplasma) were milder than those of mycoplasma infections. mNGS identified more bacterial infections when compared to the CT methods and was able to identify co-infections which were initially missed on CT. Additionally, it was able to identify pathogens that were beyond the scope of the CT methods. The mNGS method is a powerful supplement to clinical diagnostic tools in respiratory infections, as it can increase the precision of diagnosis and guide the use of antibiotics.https://www.frontiersin.org/articles/10.3389/fmed.2022.952636/fullmetagenomic next-generation sequencing (mNGS)bronchoalveolar lavage fluid (BALF)pneumoniachildrenpathogendiagnosis |
| spellingShingle | Wei Guo Wei Guo Xiaojian Cui Qiushi Wang Yupeng Wei Yanqing Guo Tongqiang Zhang Tongqiang Zhang Jianghua Zhan Jianghua Zhan Clinical evaluation of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community-acquired pneumonia Frontiers in Medicine metagenomic next-generation sequencing (mNGS) bronchoalveolar lavage fluid (BALF) pneumonia children pathogen diagnosis |
| title | Clinical evaluation of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community-acquired pneumonia |
| title_full | Clinical evaluation of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community-acquired pneumonia |
| title_fullStr | Clinical evaluation of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community-acquired pneumonia |
| title_full_unstemmed | Clinical evaluation of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community-acquired pneumonia |
| title_short | Clinical evaluation of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community-acquired pneumonia |
| title_sort | clinical evaluation of metagenomic next generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community acquired pneumonia |
| topic | metagenomic next-generation sequencing (mNGS) bronchoalveolar lavage fluid (BALF) pneumonia children pathogen diagnosis |
| url | https://www.frontiersin.org/articles/10.3389/fmed.2022.952636/full |
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