Clinical Microbiology and Antimicrobial Chemotherapy. 2026; 28(1):124-130
To investigate the bacterial and fungal microbiota of the lower respiratory tract in hospitalized patients with tuberculosis and HIV coinfection.
A total of 378 sputum samples from 147 patients at the Novosibirsk Tuberculosis Research Institute (Ministry of Health of the Russian Federation) were collected and analyzed between 2021 and 2024. Sputum samples were obtained according to standardized protocols to minimize contamination with upper respiratory tract microflora and ensure representativeness of the lower respiratory tract biota. Samples were cultured on selective medium. Microbial identification was performed by MALDItof mass spectrometry using a Microflex instrument (Bruker Daltonics, Germany). Statistical analysis was conducted using SPSS software (version 19).
To differentiate lower respiratory tract isolates from potential contaminants, paired oropharyngeal (throat) and sputum samples were compared by quantitative culture (CFU/mL) according to established clinical criteria, with adjustments for HIV status. A total of 492 pathogenic and opportunistic microorganisms, belonging to 15 families, were isolated. Fungal microbiota accounted for 44.9% of isolates, predominantly of the family Saccharomycetaceae (mainly C. albicans). Bacterial microbiota constituted 51.1%, represented by Enterobacteriaceae (21.5%), Staphylococcaceae (9.96%), Pasteurellaceae (8.94%, and Pseudomonadaceae (5.69%). The spectrum of microorganisms varied depending on the clinical forms of tuberculosis and the type of drug resistance of mycobacterium.
Conclusions.The lower respiratory tract microbiome in patients with active tuberculosis and HIV coinfection is characterized by severe dysbiosis, with a predominance of fungal taxa and Gram-negative facultative anaerobes. This dysbiosis may be associated with factors such as the drug resistance profile of Mycobacterium tuberculosis, disease duration, combination chemotherapy, and the immunosuppressive effects of HIV. These findings highlight the need for a comprehensive approach to the diagnosis and treatment of patients with pulmonary tuberculosis and concomitant HIV infection.