Cell-free DNA next-generation sequencing for Mycobacterium tuberculosis obtained from plasma of children with active tuberculosis
Abstract Background Difficulties in microbiologically confirming childhood tuberculosis (TB) can result in delayed treatment and increased disease severity. Methods In this study, we for the first time used whole genome next-generation sequencing (NGS) to detect cell-free DNA (cfDNA) from Mycobacter...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-03-01
|
| Series: | BMC Pediatrics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12887-025-05526-7 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850028060214034432 |
|---|---|
| author | Shuting Quan Xue Tian Yuting Sun Hui Qi Weiwei Jiao Baixu Sun Fang Xu Min Fang Xuemei Yang Xi Zeng Kun Duan Jichao Wang Xue Fu Li Duan Lin Sun Adong Shen |
| author_facet | Shuting Quan Xue Tian Yuting Sun Hui Qi Weiwei Jiao Baixu Sun Fang Xu Min Fang Xuemei Yang Xi Zeng Kun Duan Jichao Wang Xue Fu Li Duan Lin Sun Adong Shen |
| author_sort | Shuting Quan |
| collection | DOAJ |
| description | Abstract Background Difficulties in microbiologically confirming childhood tuberculosis (TB) can result in delayed treatment and increased disease severity. Methods In this study, we for the first time used whole genome next-generation sequencing (NGS) to detect cell-free DNA (cfDNA) from Mycobacterium tuberculosis (MTB) in plasma from children. Results We enrolled 94 children with active TB and 32 children with other respiratory infections. Combining NGS with probe capture enrichment (targeted cfNGS) showed higher coverage and detecting capability than did NGS alone. The targeted cfNGS showed slightly lower sensitivity (31.9% vs. 44.7%, P = 0.072) and specificity (96.9% vs. 100.0%, P = 0.236) to those of sputum tested using Xpert. Agreement between cfNGS-plasma and Xpert-sputum was weak (κ = 0.217). Concordant results were obtained for only 85 children (67.5%; 16 cases positive by both tests and 69 cases negative by both tests). A total of 40 children with MTB culture negative results were tested to have positive cfNGS-plasma or Xpert-sputum outcomes, yielding a significantly increased percentage of children with bacteriological evidence (20.2% [19/94] for MTB culture-positive only vs. 62.8% [59/94] for cfNGS-plasma, Xpert-sputum or culture positive). Conclusions These data suggest that cfNGS performed well for diagnosing TB using plasma from children. cfNGS may be a new method for diagnosing patients with paucibacillary TB. |
| format | Article |
| id | doaj-art-23607e65248c48ccad80a09a99b103d3 |
| institution | DOAJ |
| issn | 1471-2431 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Pediatrics |
| spelling | doaj-art-23607e65248c48ccad80a09a99b103d32025-08-20T02:59:57ZengBMCBMC Pediatrics1471-24312025-03-0125111110.1186/s12887-025-05526-7Cell-free DNA next-generation sequencing for Mycobacterium tuberculosis obtained from plasma of children with active tuberculosisShuting Quan0Xue Tian1Yuting Sun2Hui Qi3Weiwei Jiao4Baixu Sun5Fang Xu6Min Fang7Xuemei Yang8Xi Zeng9Kun Duan10Jichao Wang11Xue Fu12Li Duan13Lin Sun14Adong Shen15Laboratory of Respiratory Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing Key Laboratory of Core Technologies for the Prevention and Treatment of Emerging Infectious Diseases in Children, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s HealthLaboratory of Respiratory Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing Key Laboratory of Core Technologies for the Prevention and Treatment of Emerging Infectious Diseases in Children, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s HealthLaboratory of Respiratory Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing Key Laboratory of Core Technologies for the Prevention and Treatment of Emerging Infectious Diseases in Children, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s HealthLaboratory of Respiratory Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing Key Laboratory of Core Technologies for the Prevention and Treatment of Emerging Infectious Diseases in Children, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s HealthLaboratory of Respiratory Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing Key Laboratory of Core Technologies for the Prevention and Treatment of Emerging Infectious Diseases in Children, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s HealthLaboratory of Respiratory Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing Key Laboratory of Core Technologies for the Prevention and Treatment of Emerging Infectious Diseases in Children, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s HealthLaboratory of Respiratory Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing Key Laboratory of Core Technologies for the Prevention and Treatment of Emerging Infectious Diseases in Children, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s HealthThe No. 1 People’s Hospital of Liangshan Yizu Autonomous PrefectureLaboratory of Respiratory Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing Key Laboratory of Core Technologies for the Prevention and Treatment of Emerging Infectious Diseases in Children, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s HealthLaboratory of Respiratory Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing Key Laboratory of Core Technologies for the Prevention and Treatment of Emerging Infectious Diseases in Children, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s HealthHangzhou MatriDx Biotechnology Co., LtdHangzhou MatriDx Biotechnology Co., LtdHangzhou MatriDx Biotechnology Co., LtdThe No. 1 People’s Hospital of Liangshan Yizu Autonomous PrefectureLaboratory of Respiratory Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing Key Laboratory of Core Technologies for the Prevention and Treatment of Emerging Infectious Diseases in Children, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s HealthLaboratory of Respiratory Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing Key Laboratory of Core Technologies for the Prevention and Treatment of Emerging Infectious Diseases in Children, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s HealthAbstract Background Difficulties in microbiologically confirming childhood tuberculosis (TB) can result in delayed treatment and increased disease severity. Methods In this study, we for the first time used whole genome next-generation sequencing (NGS) to detect cell-free DNA (cfDNA) from Mycobacterium tuberculosis (MTB) in plasma from children. Results We enrolled 94 children with active TB and 32 children with other respiratory infections. Combining NGS with probe capture enrichment (targeted cfNGS) showed higher coverage and detecting capability than did NGS alone. The targeted cfNGS showed slightly lower sensitivity (31.9% vs. 44.7%, P = 0.072) and specificity (96.9% vs. 100.0%, P = 0.236) to those of sputum tested using Xpert. Agreement between cfNGS-plasma and Xpert-sputum was weak (κ = 0.217). Concordant results were obtained for only 85 children (67.5%; 16 cases positive by both tests and 69 cases negative by both tests). A total of 40 children with MTB culture negative results were tested to have positive cfNGS-plasma or Xpert-sputum outcomes, yielding a significantly increased percentage of children with bacteriological evidence (20.2% [19/94] for MTB culture-positive only vs. 62.8% [59/94] for cfNGS-plasma, Xpert-sputum or culture positive). Conclusions These data suggest that cfNGS performed well for diagnosing TB using plasma from children. cfNGS may be a new method for diagnosing patients with paucibacillary TB.https://doi.org/10.1186/s12887-025-05526-7Next-generation sequencingCell-free DNATuberculosisChildDiagnosis |
| spellingShingle | Shuting Quan Xue Tian Yuting Sun Hui Qi Weiwei Jiao Baixu Sun Fang Xu Min Fang Xuemei Yang Xi Zeng Kun Duan Jichao Wang Xue Fu Li Duan Lin Sun Adong Shen Cell-free DNA next-generation sequencing for Mycobacterium tuberculosis obtained from plasma of children with active tuberculosis BMC Pediatrics Next-generation sequencing Cell-free DNA Tuberculosis Child Diagnosis |
| title | Cell-free DNA next-generation sequencing for Mycobacterium tuberculosis obtained from plasma of children with active tuberculosis |
| title_full | Cell-free DNA next-generation sequencing for Mycobacterium tuberculosis obtained from plasma of children with active tuberculosis |
| title_fullStr | Cell-free DNA next-generation sequencing for Mycobacterium tuberculosis obtained from plasma of children with active tuberculosis |
| title_full_unstemmed | Cell-free DNA next-generation sequencing for Mycobacterium tuberculosis obtained from plasma of children with active tuberculosis |
| title_short | Cell-free DNA next-generation sequencing for Mycobacterium tuberculosis obtained from plasma of children with active tuberculosis |
| title_sort | cell free dna next generation sequencing for mycobacterium tuberculosis obtained from plasma of children with active tuberculosis |
| topic | Next-generation sequencing Cell-free DNA Tuberculosis Child Diagnosis |
| url | https://doi.org/10.1186/s12887-025-05526-7 |
| work_keys_str_mv | AT shutingquan cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis AT xuetian cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis AT yutingsun cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis AT huiqi cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis AT weiweijiao cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis AT baixusun cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis AT fangxu cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis AT minfang cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis AT xuemeiyang cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis AT xizeng cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis AT kunduan cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis AT jichaowang cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis AT xuefu cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis AT liduan cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis AT linsun cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis AT adongshen cellfreednanextgenerationsequencingformycobacteriumtuberculosisobtainedfromplasmaofchildrenwithactivetuberculosis |