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

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

39748884

DOI Digital object identifier for electronic documents.

10.3389/fcimb.2024.1492881

URI Uniform resource identifier for web resources.

Authors

Zhou H, Pei Y, Xie Q, Nie W, Liu X, Xia H, Jiang J

Journal

Frontiers in cellular and infection microbiology

Year

2024

Keywords:

bronchoalveolar lavage fluid, conventional microbial test, metagenomic next-generation sequencing, microecology, pediatric pulmonary tuberculosis

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.

Experiment 1

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Curated date: 2025/07/18

Curator: Nuerteye

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Subjects

Location of subjects: China

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Lung Pulmo,Lung,lung

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Pulmonary tuberculosis lung TB,lung tuberculosis,pulmonary TB,pulmonary tuberculosis,Tuberculosis, Pulmonary,Pulmonary tuberculosis

Group 0 name Corresponds to the control (unexposed) group for case-control studies: pediatric pneumonia patients (NTB group)

Group 1 name Corresponds to the case (exposed) group for case-control studies: pediatric pulmonary tuberculosis (PTB group)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: showing positive TB culturing, TB-PCR, or mNGS result

Group 0 sample size Number of subjects in the control (unexposed) group: 21

Group 1 sample size Number of subjects in the case (exposed) group: 43

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Signature 1

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Curated date: 2025/07/18

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Source: Figures 3F, G; Supplementary Table 2

Description: LEfSe analysis was performed to identify differentially abundant taxa, which are highlighted on the phylogenetic tree in cladogram format (F) and for which the linear discriminant analysis scores are shown (G)

Abundance in Group 1: increased abundance in pediatric pulmonary tuberculosis (PTB group)

NCBI	Quality Control	Links
Gordonia polyisoprenivorans
Mycobacterium tuberculosis
Aquirufa antheringensisAquirufa antheringensis
Flavobacterium ammoniigenesFlavobacterium ammoniigenes
Aquirufa lenticrescensAquirufa lenticrescens
Rahnella sikkimica
Candidatus Planktophila sulfonicaCandidatus Planktophila sulfonica

Revision editor(s): Nuerteye

Signature 2

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Mark reviewed

Your review change was submitted

Needs review

Curated date: 2025/07/18

Curator: Nuerteye

Revision editor(s): Nuerteye

Source: Figures 3F, G; Supplementary Table 2

Description: LEfSe analysis was performed to identify differentially abundant taxa, which are highlighted on the phylogenetic tree in cladogram format (F) and for which the linear discriminant analysis scores are shown (G)

Abundance in Group 1: decreased abundance in pediatric pulmonary tuberculosis (PTB group)

NCBI	Quality Control	Links
Moraxella nonliquefaciensMoraxella nonliquefaciens
Enterobacter quasiroggenkampiiEnterobacter quasiroggenkampii
Moraxella_nonliquefaciensMoraxella_nonliquefaciens
Pseudomonas putida
Aeromonas sp FDAARGOS 1408Aeromonas sp FDAARGOS 1408
Moraxella catarrhalis
Aquitalea magnusoniiAquitalea magnusonii
Massilia LPB0304Massilia LPB0304
Chromobacterium sp ATCC 53434Chromobacterium sp ATCC 53434
Rhodococcus opacus

Revision editor(s): Nuerteye