Pre- and Post-treatment Lung Microbiota, Metabolome and Immune Signatures at the Site of Disease in Patients With Active Pulmonary Tuberculosis
Pre- and Post-treatment Lung Microbiota, Metabolome and Immune Signatures at the Site of Disease in Patients With Active Pulmonary Tuberculosis
The diverse microbial communities in different parts of the human body (microbiome) are
 important for health but understudied in pulmonary tuberculosis (TB), which is the single
 biggest infectious cause of death in the world. The investigators will study the
 site-of-disease microbiome (in the lung bronchoalveolar space) in TB cases to investigate
 how, before TB treatment, metabolic compounds made by microbes affect host biomarkers
 important for TB control. The investigators will ask this question again at the
 end-of-treatment and one year later. Specifically, the investigators will sample the lung at
 the active TB hotspot identified by imaging and compare this to a non-involved lung segment
 usually in the opposite lung. The investigators will compare the lung microbiome to other
 sites in the body (i.e. oral cavity, nasopharynx, supraglottis, and gut). A small amount of
 blood (~15 ml) will be collected to assess peripheral immunological correlates of the host
 microbiome. Protected specimen brushings of the lung will be used to explore transcriptomic
 signatures and how these relate to the lung microbiome. The investigators will also apply
 these questions to the same number of controls (healthy patients and patients with an
 alternative diagnoses). This will lay the foundation for clinical trials to evaluate if
 specific bacteria have diagnostic (e.g., PCR) or therapeutic potential (e.g., antibiotics,
 prebiotics, probiotics, vaccines) where targeting the microbiome could improve clinical
 outcomes.
The human body is host to complex microbial communities at different anatomical sites such as
 the gut, oral cavity, vagina, skin, and the lower respiratory tract - a site previously
 thought to be sterile. Growing evidence has implicated the role of the human microbiome in
 various diseases for example, Prevotella-enriched lung communities in HIV-positive pneumonia
 patients independently predict 70-day mortality, and Lactobacillus enriched murine gut
 microbiome alleviates asthma-like symptoms. However, despite the scale and severity of TB,
 there are limited studies on the microbiome in TB cases, the site of disease, and the effect
 of treatment, especially in the context of HIV. These key knowledge gaps preclude the design
 and evaluation of interventions that could target the microbiome and avert poor treatment
 outcomes in TB.

 To date the few microbiome studies in TB have focused on the upper respiratory tract (using
 specimens such as sputum) and gut rather than the site of disease which, in TB, is typically
 the lung. These studies have shown associations between the microbiome and state of disease.
 For example, mice colonized with Helicobacter hepaticus in the gut demonstrate poor control
 of mycobacterial growth, heightened inflammation, and severe tissue pathology in the lungs.
 The lung which is the site of disease in pulmonary TB has been widely considered sterile
 until recently and the lung microbiome remains widely understudied in TB regardless of the
 potential impact it might have in TB pathogenesis. One of the major reasons why the lung is
 understudied is the difficult in sampling the lung. The investigators will implement a
 modified bronchoscopy procedure to avoid microbial cross-contamination from neighbouring
 anatomical sites (including from diseased to healthy parts of the lungs) and to accurately
 sample the low biomass in the bronchoalveolar space. The investigators hypothesize that TB
 cases have a distinct site-of-disease lung microbiota compared to non-diseased contralateral
 tissue, characterized by an enrichment of oral anaerobic fermenters, SCFAs, and impaired
 inflammation and tissue repair biomarkers. They also expect microbial and host biomarkers to
 be altered by TB treatment. A study by one of the investigators has already demonstrated lung
 microbiomes enriched with anaerobic oral taxa are associated with lung inflammation of the
 Th17 phenotype. The products of microbial anaerobic metabolism have also been shown to
 modulate immune response to diseases. The investigators will correlate the complex microbial
 communities at the site-of-disease in TB with the microbial and host biomarkers at the
 site-of-disease.

 The study will recruit self-reporting patients with their first TB episode and Xpert MTB/RIF
 Ultra-confirmed TB from Scottsdene and Wallacedene primary care clinics in Cape Town. A total
 of 50 TB cases equally stratified by HIV status and 50 healthy household contacts (HHC) also
 stratified by HIV will be recruited. In addition to HIV-negatives, the study is recruiting an
 equal number of ART-treated HIV-positive TB cases, because there an epidemiologically
 important subpopulation with impaired pulmonary immunity. An additional 50 sick controls with
 other pulmonary diseases (Asthma, Chronic obstructive pulmonary disease (COPD), Cancer,
 Bronchiectasis (including post-TB) and Pneumonia) will recruited as comparator groups.
Inclusion Criteria:

 -  18-60 years old.

 -  Agree to undergo CXR and/or CT scan.

 -  Has unilateral TB disease defined as one lung with extensive evidence of TB disease
 (non-applicable to healthy controls; sick controls will require an alternative
 diagnosis).

 -  No evidence of prior TB treatment and/or CXR/CT does not have obvious evidence of
 prior TB.

 -  Willing to undergo a research bronchoscopy at baseline, 6 months and 18 months and
 likely to remain in the area for the study period.

 -  If HIV-positive, must be stable on antiretroviral therapy (ART) for ≥1 year.

 -  Able and willing to return for follow-up visits, with no plans to move in the near
 future.

 -  Willing to comply with study requirements i.e. provision of contact details and
 written, informed consent prior to enrolment.

 Exclusion Criteria:

 -  Less than 18 years or older than 60 years of age.

 -  Has already initiated TB treatment.

 -  Rifampicin resistant.

 -  Has a previous history of TB.

 -  Bilateral TB disease defined as both lungs with extensive TB disease

 -  Has received probiotics, antibiotics or inhaled steroids within three months prior to
 enrolment (not applicable to sick controls)

 -  Has diabetes mellitus, which affects TB disease, treatment response, and the
 microbiome

 -  Has a contraindication for bronchoscopy (e.g., FEV1 <70%), as determined by
 bronchoscopists according to best practice guidelines

 -  Has a daily alcohol intake of more than 6 beers or 4 mixed drinks

 -  Is pregnant (a commercial human chorionic gonadotropin determination assay will be
 performed in accordance with manufacturer's guidance on urine) or pregnancy planned
 for follow-up period

 -  Recent hospitalization for any reason