Abstract:

Objective: To explore the differences in the distribution of microbial communities in the lower respiratory tract among patients with pulmonary tuberculosis, other pathogenic infections, and non-infectious pulmonary diseases. Methods: In this retrospective study, 83 patients suspected of having pulmonary tuberculosis, admitted to Beijing Jishuitan Hospital affiliated with Capital Medical University and Peking University People’s Hospital between March 1, 2021, and February 28, 2023, were selected for analysis. All study subjects were negative for sputum smears and T-SPOT.TB tests, and received bronchoscopy with bronchoalveolar lavage as per standard diagnostic procedures. Pathogen testing on bronchoalveolar lavage fluid (BALF) included metagenomic next-generation sequencing, GeneXpert MTB/RIF assays, and conventional bacterial and fungal cultures. Basic patient information and laboratory test results were collected via the electronic medical record system, enabling the analysis of lower respiratory tract microbiota characteristics across diverse patient groups. Results: Following pathogenetic analysis, the cohort was categorized into tuberculosis (28 patients), pneumonia (38 patients), and non-infection groups (17 patients). Examination of microbial abundance and diversity within the lower respiratory tract revealed median Shannon indices of 1.2864 (IQR: 0.3021, 1.9459), 1.1032 (IQR: 0.3725, 1.7711), and 1.2049 (IQR: 0.6873, 1.9974) for the tuberculosis, pneumonia, and non-infection groups respectively. Similarly, median Simpson indices were 0.5693 (IQR: 0.1346, 0.8259), 0.5503 (IQR: 0.1900, 0.7533), and 0.5141 (IQR: 0.3065, 0.7507), and Chao1 indices were 8.50 (IQR: 3.00, 20.75), 7.50 (IQR: 3.25, 18.75), and 7.00 (IQR: 2.00, 22.00) respectively, with no significant statistical differences noted (H-values of 0.130, 0.208, 0.235; P-values of 0.973, 0.901, and 0.889). β-Diversity analysis showed a dispersed distribution within the tuberculosis group indicating notable within-group heterogeneity, whereas the pneumonia and non-infection groups exhibited extensive overlap. Pathogenic microbial community analysis indicated heightened prevalence of Firmicutes, Staphylococcus, and Streptococcus in tuberculosis group samples; Bacteroidetes, Proteobacteria, Corynebacterium, Enterococcus, and Pseudomonas were notably prevalent in pneumonia group samples; whereas Actinobacteria, Fusobacteria, and respiratory colonizers such as Rothia and Neisseria showed increased abundance in non-infection group samples. LEfSe analysis revealed significant enrichment of Mycobacterium tuberculosis, Streptococcus mucosus, and atypical Veillonella in the tuberculosis group; Corynebacterium striatum, Klebsiella pneumoniae, and Pseudomonas maltophilia were prominently enriched in the pneumonia group; in contrast, the non-infection group exhibited a diversification of 12 microbial species, marking a notable deviation from the pathogenic profiles observed in the tuberculosis and pneumonia groups and bearing closer resemblance to the microbiota of the upper respiratory tract. Conclusion: Infection with Mycobacterium tuberculosis influences the distribution of microbial communities in the lower respiratory tract, exerting minimal effects on α diversity. Notably, its impact on β diversity significantly surpasses that observed in pneumonia caused by other pathogens and in non-infectious pulmonary conditions.

Key words: Mycobacterium tuberculosis, Respiratory tract infections, Bronchoalveolar lavage fluid, Sequence analysis, DNA, Biodiversity