Lung Microbiota in People Diagnosed with HIV and Pneumonia: A Colombian Cohort Study

The lung microbiota plays a key role in respiratory health, but its composition in individuals living with HIV and diagnosed with community-acquired pneumonia (CAP) remains underexplored. A prospective cohort study in Medellín, Colombia recruited individuals with CAP and/or HIV between 2016 and 2018. Clinical and microbiological data were collected at baseline, with bronchoalveolar lavage samples obtained at baseline and induced sputum samples collected at baseline and 6-month follow-up. Microbiota composition was analyzed in these samples using Illumina MiSeq sequencing of the 16S ribosomal RNA gene. Among 248 screened participants, 64 were included: HIV and CAP (n = 27), CAP (n = 7), and HIV (n = 30); 70.3% were males, and 76.6% were between 25 and 64 years old. The HIV and CAP group had a lower proportion of receiving antiretroviral treatment and a higher prevalence of advanced immunosuppression. The most frequent micro-organisms identified by conventional methods in the HIV and CAP group were Mycobacterium tuberculosis (40.7%) and Pneumocystis jirovecii (18.5%). The dominant phyla (Firmicutes, Proteobacteria, Fusobacteria, Bacteroidetes, and Actinobacteria) and genera (Streptococcus, Haemophilus, Veillonella, Neisseria, and Fusobacterium) were identified in the overall study population, including both baseline and 6-month follow-up samples. The HIV and CAP group showed changes in bacterial diversity and relative abundance over 6 months. These findings provide insights into the dynamic lung microbiota in individuals coinfected with HIV and CAP, highlighting the impact of HIV and CAP on microbial composition and diversity, which may inform future studies exploring clinical outcomes.