Diagnosis and insight into the unique lung microbiota of pediatric pulmonary tuberculosis patients by bronchoalveolar lavage using metagenomic next-generation sequencing

Haiyi Zhou; Yi Pei; Qifang Xie; Wenjie Nie; Xiaoyan Liu; Han Xia; Jie Jiang

doi:10.3389/fcimb.2024.1492881

Diagnosis and insight into the unique lung microbiota of pediatric pulmonary tuberculosis patients by bronchoalveolar lavage using metagenomic next-generation sequencing

Front Cell Infect Microbiol. 2024 Dec 19:14:1492881. doi: 10.3389/fcimb.2024.1492881. eCollection 2024.

Authors

Haiyi Zhou^#^{1

2}, Yi Pei^#^{1

3}, Qifang Xie^{1

2}, Wenjie Nie^{1

2}, Xiaoyan Liu^{1

2}, Han Xia⁴, Jie Jiang^{1

2

3

5}

Affiliations

¹ The Affiliated Changsha Central Hospital, Department of Center for Tuberculosis Diagnosis and Treatment, Hengyang Medical School, University of South China, Changsha, China.
² Changsha Tuberculosis Technology Innovation Center of Children, Hengyang Medical School, University of South China, Changsha, Hunan, China.
³ Hunan Clinical Medical Technology Demonstration Base of Tuberculosis Diagnosis and Treatment, Hengyang Medical School, University of South China, Changsha, Hunan, China.
⁴ Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China.
⁵ Key Laboratory of Rare Pediatric Diseases, Ministry of Education, Hengyang Medical School, University of South China, Changsha, China.

^# Contributed equally.

Abstract

Background: Although previous studies have reported the dysregulation of respiratory tract microbiota in infectious diseases, insufficient data exist regarding respiratory microbiota imbalances in the lower respiratory tracts of children with pulmonary tuberculosis (PTB). In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of PTB patients using bronchoalveolar lavage fluid (BALF) samples.

Methods: A total of 64 participants, comprising 43 pediatric PTB and 21 pediatric pneumonia patients were recruited in the present study. BALF samples were collected from the above participants. Parallel comparisons between mNGS and conventional microbial test (CMT) pathogen detection were performed. Moreover, the diversity and structure of all 64 patients' lung BALF microbiomes were explored using the mNGS data.

Results: Comparing to the final clinical diagnosis, mNGS in BALF samples produced a sensitivity of 46.51%, which was lower than that of TB-PCR (55.00%) and Xpert (55.00%). The diagnostic efficacy of PTB can be highly enhanced by mNGS combined with TB-PCR (AUC=0.8140, P<0.0001). There were no significant differences in the diversity either between patients with TB and pneumonia. Positive mNGS pathogen results in pediatric PTB patients significantly affect the β-diversity of the pulmonary microbiota. In addition, significant taxonomic differences were found in BALF specimens from patients with PTB and pneumonia, both of which have unique bacterial compositions.

Conclusions: mNGS is valuable in the etiological diagnosis of PTB, and can reveal pulmonary microecological characteristics. For pediatric PTB patients, the mNGS should be implemented early and complementary to CMTs.

Keywords: bronchoalveolar lavage fluid; conventional microbial test; metagenomic next-generation sequencing; microecology; pediatric pulmonary tuberculosis.

MeSH terms

Adolescent
Bronchoalveolar Lavage
Bronchoalveolar Lavage Fluid* / microbiology
Child
Child, Preschool
Female
High-Throughput Nucleotide Sequencing*
Humans
Infant
Lung* / microbiology
Male
Metagenomics* / methods
Microbiota* / genetics
Mycobacterium tuberculosis / genetics
Mycobacterium tuberculosis / isolation & purification
RNA, Ribosomal, 16S / genetics
Sensitivity and Specificity
Tuberculosis, Pulmonary* / diagnosis
Tuberculosis, Pulmonary* / microbiology

Substances

RNA, Ribosomal, 16S

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the Natural Science Foundation of Hunan Province (grant numbers 2023JJ60405); the Changsha Guiding Science and Technology Plan Project (grant numbers KZD22073); and supported by the Key Project of Changsha Central Hospital Technology Plan (grant numbers YNKY202303).