The lung microbiome of Human Immunodeficiency Virus-infected patients with active pulmonary Mycobacterium tuberculosis infection

Abstract

Despite being one of the oldest known bacteria to cause disease in man, Mycobacterium. tuberculosis (M. tuberculosis) claims in excess of a million lives each year and continues to be a topic of research. The lung microbiome, in contrast, is a relatively novel area of research which has come about after next-generation sequencing methods have disproven the theory that the lungs were sterile sites in the absence of disease.

This study was the first to describe the lung microbiome in patients with human immunodeficiency virus (HIV) and M. tuberculosis co-infection, using high-quality sputum specimens and broncho-alveolar lavage fluid (BALF). There were three study groups: (i) a control group with HIV but no respiratory diseases, (ii) a group with HIV and pneumonia who were culture negative for tuberculosis (TB) and (iii) a group with HIV and pneumonia who were culture positive for TB.

The phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes dominated the lung microbiome of patients with TB. A novel finding was that Burkholderia was over-represented in the lung microbiome of patients with TB, which requires further study to understand the pathogenesis, interaction with TB and role in subsequent chronic lung disease. Mycobacterium tuberculosis was not the dominant bacteria in patients with TB, this may be due to under-estimation of its presence by 16S and the DNA extraction methods used, or may indicate that the functional relationships of TB in the lung microbiome are more important in the survival of M. tuberculosis. This study looked at the clinical characteristics and outcomes of patients with HIV and severe pneumonia. One hundred and seventeen patients with HIV and pneumonia were screened for inclusion in the study. Fifty-one met inclusion criteria for the microbiome study, but all 117 were included in the clinical part of the study. Patients had a high mortality rate, long hospital stays and were often not on highly active antiretroviral therapy (HAART). There is an indication that lung ultrasound is useful in patients who have HIV and pneumonia, particularly in the context of B-lines predicting Pneumocystis jirovecii as the causative organism.

There was a loss of alpha and beta diversity in the lung microbiome of patients with M. tuberculosis infection when compared with the control group (i). However, no statistically significant differences in diversity could be found between the group with pneumonia (ii) and the group with TB (iii) when all specimens were considered.

Different specimen types (sputum and BALF) were compared as a means to study the lung microbiome in TB. When comparing specimens by disease type (pneumonia vs TB) a greater degree of dysbiosis in the TB group could be proven when BALF specimens were compared, but not when sputum was compared. The BALF in patients with TB revealed over-representation of the genus Stenotrophomonas.

Lastly the pro-inflammatory cytokine profiles - tumour necrosis factor-α (TNF-α), interferon-γ (IFN- γ), interleukin 6 (IL-6), interleukin 8 (IL-8) and interferon-γ induced protein 10 (IP-10) - of sputum specimens from all three groups of patients were investigated. The results showed a clear over-expression of IP-10 in the patients with TB.

This research was the first to describe the lung microbiome in the context of HIV and TB co-infection. Dysbiosis in the lung microbiome was proven and it was illustrated that BALF was superior in demonstrating dysbiosis in patients with pulmonary TB. Future research is needed to better define the role of the microbiome in the pathogenesis and progression of respiratory disease caused by M. tuberculosis and how the microbiome may be manipulated to enhance treatment of the disease.