Application of Metagenomic Next-Generation Sequencing (mNGS) Using Bronchoalveolar Lavage Fluid (BALF) in Diagnosing Pneumonia of Children
ABSTRACT Pneumonia is the leading cause of death in children; the pathogens are often difficult to diagnose. In this study, the performance of metagenomic next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) samples from 112 children with confirmed pneumonia has been evaluated...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2022-10-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01488-22 |
| _version_ | 1811329690439254016 |
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| author | Aimei Yang Chen Chen Yan Hu Guilang Zheng Peiling Chen Zhiwei Xie Huifeng Fan Yueyu Sun Peiqiong Wu Wenhui Jiang Chun Wang Jingwen Zhang Dongwei Zhang Jing Wang Xiaoyin Hu Han Xia Genquan Yin Yuxiong Guo |
| author_facet | Aimei Yang Chen Chen Yan Hu Guilang Zheng Peiling Chen Zhiwei Xie Huifeng Fan Yueyu Sun Peiqiong Wu Wenhui Jiang Chun Wang Jingwen Zhang Dongwei Zhang Jing Wang Xiaoyin Hu Han Xia Genquan Yin Yuxiong Guo |
| author_sort | Aimei Yang |
| collection | DOAJ |
| description | ABSTRACT Pneumonia is the leading cause of death in children; the pathogens are often difficult to diagnose. In this study, the performance of metagenomic next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) samples from 112 children with confirmed pneumonia has been evaluated. mNGS performed a significantly higher positive detection rate (91.07%, 95% confidence interval [CI] 83.80% to 95.40%) and coincidence rate against the final diagnosis (72.32%, 95% CI 62.93% to 80.15%) than that of conventional methods (70.54%, 95% CI 61.06% to 78.58% and 56.25%, 95% CI 46.57% to 65.50%, respectively) (P < 0.01 and P < 0.05, respectively). Bacteria, viruses, and their mixed infections were common in children with pneumonia. Streptococcus pneumoniae was the most common bacterial pathogen in children with pneumonia, while Haemophilus parainfluenzae and Haemophilus influenzae seemed more likely to cause nonsevere pneumonia in children. In contrast, human cytomegalovirus (CMV) infection and the simultaneous bacterial infections could cause severe pneumonia, especially in children with underlying diseases. After adjustments of antibiotics based on mNGS and conventional methods, the conditions improved in 109 (97.32%) children. mNGS of BALF samples has shown great advantages in diagnosing the pathogenic etiology of pneumonia in children, especially when considering the limited volumes of BALF and the previous use of empirical antibiotics, contributing to the timely adjustment of antibiotic treatments, which can potentially improve the prognosis and decrease the mortality. IMPORTANCE Our study indicates high efficiency of mNGS using BALF for the detection of causative pathogens that cause pneumonia in children. mNGS can be a potential diagnostic tool to supplement conventional methods for children’s pneumonia. |
| first_indexed | 2024-04-13T15:48:23Z |
| format | Article |
| id | doaj.art-29d9d24b2b514881b7b2c00dded5f648 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-04-13T15:48:23Z |
| publishDate | 2022-10-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-29d9d24b2b514881b7b2c00dded5f6482022-12-22T02:40:54ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972022-10-0110510.1128/spectrum.01488-22Application of Metagenomic Next-Generation Sequencing (mNGS) Using Bronchoalveolar Lavage Fluid (BALF) in Diagnosing Pneumonia of ChildrenAimei Yang0Chen Chen1Yan Hu2Guilang Zheng3Peiling Chen4Zhiwei Xie5Huifeng Fan6Yueyu Sun7Peiqiong Wu8Wenhui Jiang9Chun Wang10Jingwen Zhang11Dongwei Zhang12Jing Wang13Xiaoyin Hu14Han Xia15Genquan Yin16Yuxiong Guo17Department of Pediatric Intensive Care Unit, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, ChinaPediatric Respiratory Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, ChinaDepartment of Pediatric Intensive Care Unit, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, ChinaDepartment of Pediatric Intensive Care Unit, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, ChinaDepartment of Pediatric Intensive Care Unit, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, ChinaPediatric Respiratory Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, ChinaPediatric Respiratory Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, ChinaDepartment of Pediatric Intensive Care Unit, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, ChinaPediatric Respiratory Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, ChinaPediatric Respiratory Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, ChinaDepartment of Pediatric Intensive Care Unit, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, ChinaDepartment of Pediatric Intensive Care Unit, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, ChinaPediatric Respiratory Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, ChinaDepartment of Pediatric Intensive Care Unit, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, ChinaPediatric Respiratory Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, ChinaDepartment of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, ChinaPediatric Respiratory Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, ChinaDepartment of Pediatric Intensive Care Unit, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, ChinaABSTRACT Pneumonia is the leading cause of death in children; the pathogens are often difficult to diagnose. In this study, the performance of metagenomic next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) samples from 112 children with confirmed pneumonia has been evaluated. mNGS performed a significantly higher positive detection rate (91.07%, 95% confidence interval [CI] 83.80% to 95.40%) and coincidence rate against the final diagnosis (72.32%, 95% CI 62.93% to 80.15%) than that of conventional methods (70.54%, 95% CI 61.06% to 78.58% and 56.25%, 95% CI 46.57% to 65.50%, respectively) (P < 0.01 and P < 0.05, respectively). Bacteria, viruses, and their mixed infections were common in children with pneumonia. Streptococcus pneumoniae was the most common bacterial pathogen in children with pneumonia, while Haemophilus parainfluenzae and Haemophilus influenzae seemed more likely to cause nonsevere pneumonia in children. In contrast, human cytomegalovirus (CMV) infection and the simultaneous bacterial infections could cause severe pneumonia, especially in children with underlying diseases. After adjustments of antibiotics based on mNGS and conventional methods, the conditions improved in 109 (97.32%) children. mNGS of BALF samples has shown great advantages in diagnosing the pathogenic etiology of pneumonia in children, especially when considering the limited volumes of BALF and the previous use of empirical antibiotics, contributing to the timely adjustment of antibiotic treatments, which can potentially improve the prognosis and decrease the mortality. IMPORTANCE Our study indicates high efficiency of mNGS using BALF for the detection of causative pathogens that cause pneumonia in children. mNGS can be a potential diagnostic tool to supplement conventional methods for children’s pneumonia.https://journals.asm.org/doi/10.1128/spectrum.01488-22metagenomic next-generation sequencing (mNGS)bronchoalveolar lavage fluid (BALF)pneumoniachildrenculturediagnosis |
| spellingShingle | Aimei Yang Chen Chen Yan Hu Guilang Zheng Peiling Chen Zhiwei Xie Huifeng Fan Yueyu Sun Peiqiong Wu Wenhui Jiang Chun Wang Jingwen Zhang Dongwei Zhang Jing Wang Xiaoyin Hu Han Xia Genquan Yin Yuxiong Guo Application of Metagenomic Next-Generation Sequencing (mNGS) Using Bronchoalveolar Lavage Fluid (BALF) in Diagnosing Pneumonia of Children Microbiology Spectrum metagenomic next-generation sequencing (mNGS) bronchoalveolar lavage fluid (BALF) pneumonia children culture diagnosis |
| title | Application of Metagenomic Next-Generation Sequencing (mNGS) Using Bronchoalveolar Lavage Fluid (BALF) in Diagnosing Pneumonia of Children |
| title_full | Application of Metagenomic Next-Generation Sequencing (mNGS) Using Bronchoalveolar Lavage Fluid (BALF) in Diagnosing Pneumonia of Children |
| title_fullStr | Application of Metagenomic Next-Generation Sequencing (mNGS) Using Bronchoalveolar Lavage Fluid (BALF) in Diagnosing Pneumonia of Children |
| title_full_unstemmed | Application of Metagenomic Next-Generation Sequencing (mNGS) Using Bronchoalveolar Lavage Fluid (BALF) in Diagnosing Pneumonia of Children |
| title_short | Application of Metagenomic Next-Generation Sequencing (mNGS) Using Bronchoalveolar Lavage Fluid (BALF) in Diagnosing Pneumonia of Children |
| title_sort | application of metagenomic next generation sequencing mngs using bronchoalveolar lavage fluid balf in diagnosing pneumonia of children |
| topic | metagenomic next-generation sequencing (mNGS) bronchoalveolar lavage fluid (BALF) pneumonia children culture diagnosis |
| url | https://journals.asm.org/doi/10.1128/spectrum.01488-22 |
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