Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing
Background: Severe community-acquired pneumonia was associated with high morbidity and mortality in children. However, species-level microbiome of lower airway was sparse, and we used shotgun metagenomic next-generation sequencing to explore microbial signatures. Methods: We conducted a prospective...
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Elsevier
2025-02-01
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| Series: | Journal of Microbiology, Immunology and Infection |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1684118224002172 |
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| author | Ting-Yu Yen Ching Hsu Ni-Chung Lee Chao-Szu Wu Hsin Wang Kuan-Yi Lee Chia-Ray Lin Chun-Yi Lu Mo-Li Tsai Tzu-Yu Liu Che Lin Chien-Yu Chen Luan-Yin Chang Feipei Lai Li-Min Huang |
| author_facet | Ting-Yu Yen Ching Hsu Ni-Chung Lee Chao-Szu Wu Hsin Wang Kuan-Yi Lee Chia-Ray Lin Chun-Yi Lu Mo-Li Tsai Tzu-Yu Liu Che Lin Chien-Yu Chen Luan-Yin Chang Feipei Lai Li-Min Huang |
| author_sort | Ting-Yu Yen |
| collection | DOAJ |
| description | Background: Severe community-acquired pneumonia was associated with high morbidity and mortality in children. However, species-level microbiome of lower airway was sparse, and we used shotgun metagenomic next-generation sequencing to explore microbial signatures. Methods: We conducted a prospective cohort study to recruit children under 18 who required admission to an intensive care unit for community-acquired pneumonia between December 2019 and February 2022. Lower respiratory specimens were collected on admission for shotgun metagenomic sequencing. The children were divided into two groups. Critical cases were patients with respiratory failure requiring endotracheal ventilator support, and severe cases did not require intubation. Signatures of lower respiratory tract microbiome were compared between groups using an exact k-mer matching metagenomic analysis pipeline (Kraken 2) and a metagenome-assembled genomes pipeline (MetaWRAP). Results: Totally 66 children were enrolled, and 27 children were critical cases, and the rest were severe cases. There were significant differences in microbial community structure between different severity groups, and microbial abundance was negatively correlated with disease severity. The results showed that Haemophilus influenzae was more prominent in children who were critical, accompanied with increased expression of intracellular transport, secretion, and vesicle transport genes. Rothia mucilaginosa, Dolosigranulum pigrum, and Prevotella melaninogenica tended to be present in less severe community-acquired pneumonia group. Conclusion: This study demonstrated that significantly different microbial community was associated with severity of community-acquired pneumonia requiring intensive care admission. Species-level shotgun metagenomic sequencing facilitates the exploration of potentially pathogenic or protective microbes and shed the light of probiotic development in lower respiratory tract. |
| format | Article |
| id | doaj-art-3e73408151d14fe2b837d8512d4e9823 |
| institution | Kabale University |
| issn | 1684-1182 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Microbiology, Immunology and Infection |
| spelling | doaj-art-3e73408151d14fe2b837d8512d4e98232025-02-06T05:11:21ZengElsevierJournal of Microbiology, Immunology and Infection1684-11822025-02-015818693Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencingTing-Yu Yen0Ching Hsu1Ni-Chung Lee2Chao-Szu Wu3Hsin Wang4Kuan-Yi Lee5Chia-Ray Lin6Chun-Yi Lu7Mo-Li Tsai8Tzu-Yu Liu9Che Lin10Chien-Yu Chen11Luan-Yin Chang12Feipei Lai13Li-Min Huang14Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, TaiwanGraduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, TaiwanDepartment of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, TaiwanDepartment of Medical Genetics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, TaiwanGraduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, TaiwanDepartment of Electrical Engineering, National Taiwan University, Taipei, TaiwanDepartment of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, TaiwanDepartment of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, TaiwanDepartment of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, TaiwanGraduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan; Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan; Smart Medicine and Health Informatics Program, National Taiwan University, Taipei, TaiwanDepartment of Electrical Engineering, National Taiwan University, Taipei, Taiwan; Smart Medicine and Health Informatics Program, National Taiwan University, Taipei, Taiwan; Center for Advanced Computing and Imaging in Biomedicine, National Taiwan University, Taipei, TaiwanSmart Medicine and Health Informatics Program, National Taiwan University, Taipei, Taiwan; Center for Advanced Computing and Imaging in Biomedicine, National Taiwan University, Taipei, Taiwan; Department of Biomechatronics Engineering, National Taiwan University, Taipei, TaiwanDepartment of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan; Corresponding author. No. 8, Chung Shan S. Rd., Taipei, 10041, Taiwan.Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan; Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan; Department of Computer Science and Information Engineering, National Taiwan University, Taipei, TaiwanDepartment of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan; Corresponding author. No. 8, Chung Shan S. Rd., Taipei, 10041, Taiwan.Background: Severe community-acquired pneumonia was associated with high morbidity and mortality in children. However, species-level microbiome of lower airway was sparse, and we used shotgun metagenomic next-generation sequencing to explore microbial signatures. Methods: We conducted a prospective cohort study to recruit children under 18 who required admission to an intensive care unit for community-acquired pneumonia between December 2019 and February 2022. Lower respiratory specimens were collected on admission for shotgun metagenomic sequencing. The children were divided into two groups. Critical cases were patients with respiratory failure requiring endotracheal ventilator support, and severe cases did not require intubation. Signatures of lower respiratory tract microbiome were compared between groups using an exact k-mer matching metagenomic analysis pipeline (Kraken 2) and a metagenome-assembled genomes pipeline (MetaWRAP). Results: Totally 66 children were enrolled, and 27 children were critical cases, and the rest were severe cases. There were significant differences in microbial community structure between different severity groups, and microbial abundance was negatively correlated with disease severity. The results showed that Haemophilus influenzae was more prominent in children who were critical, accompanied with increased expression of intracellular transport, secretion, and vesicle transport genes. Rothia mucilaginosa, Dolosigranulum pigrum, and Prevotella melaninogenica tended to be present in less severe community-acquired pneumonia group. Conclusion: This study demonstrated that significantly different microbial community was associated with severity of community-acquired pneumonia requiring intensive care admission. Species-level shotgun metagenomic sequencing facilitates the exploration of potentially pathogenic or protective microbes and shed the light of probiotic development in lower respiratory tract.http://www.sciencedirect.com/science/article/pii/S1684118224002172ChildrenCommunity-acquired pneumoniaLower respiratory tractMetagenomic sequencingMicrobiome |
| spellingShingle | Ting-Yu Yen Ching Hsu Ni-Chung Lee Chao-Szu Wu Hsin Wang Kuan-Yi Lee Chia-Ray Lin Chun-Yi Lu Mo-Li Tsai Tzu-Yu Liu Che Lin Chien-Yu Chen Luan-Yin Chang Feipei Lai Li-Min Huang Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing Journal of Microbiology, Immunology and Infection Children Community-acquired pneumonia Lower respiratory tract Metagenomic sequencing Microbiome |
| title | Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing |
| title_full | Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing |
| title_fullStr | Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing |
| title_full_unstemmed | Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing |
| title_short | Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing |
| title_sort | signatures of lower respiratory tract microbiome in children with severe community acquired pneumonia using shotgun metagenomic sequencing |
| topic | Children Community-acquired pneumonia Lower respiratory tract Metagenomic sequencing Microbiome |
| url | http://www.sciencedirect.com/science/article/pii/S1684118224002172 |
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