Abstract:
Tuberculosis poses one of the greatest infectious disease threats of our time, especially when
associated with human immunodeficiency virus (HIV) infection. Very little data is available on the
lung microbiome in pulmonary tuberculosis (PTB) in HIV-positive patients. Three patient cohorts were
studied: (i) HIV-positive with no respiratory disease (control cohort), (ii) HIV-positive with pneumonia
and (iii) HIV-positive with PTB. Sputum specimens were collected in all patients and where possible a
paired BALF was collected. DNA extraction was performed using the QIAamp DNA mini kit (QIAGEN,
Germany) and extracted DNA specimens were sent to Inqaba Biotechnical Industries (Pty) Ltd for
16S rRNA gene sequence analysis using the Illumina platform (Illumina Inc, USA). Data analysis was
performed using QIMME II and R Studio version 3.6.2 (2020). The lung microbiomes of patients with
PTB, in the context of HIV co-infection, were dominated by Proteobacteria, Firmicutes, Actinobacteria
and Bacteroidetes. Loss of biodiversity and dysbiosis was found in these patients when compared
to the HIV-positive control cohort. Microbial community structure was also distinct from the control
cohort, with the dominance of genera such as Achromobacter, Mycobacterium, Acinetobacter,
Stenotrophomonas and Pseudomonas in those patients with PTB. This is the first study to describe
the lung microbiome in patients with HIV and PTB co-infection and to compare findings with an HIVpositive
control cohort. The lung microbiomes of patients with HIV and PTB were distinct from the
HIV-positive control cohort without PTB, with an associated loss of microbial diversity.
