Browsing by Author "Nyawo, Georgina Rumbidzai"

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    The microbiome and inferred function in pulmonary and extrapulmonary tuberculosis.
    (Stellenbosch : Stellenbosch University,, 2023-12) Nyawo, Georgina Rumbidzai; Theron, Grant; Naidoo, Charissa; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Biomedical Sciences. Molecular Biology and Human Genetics.
    ENGLISH ABSTRACT: Background (Chapter 1): Each year, up to 3–4% of all deaths worldwide are attributable to infection with the bacterial pathogen Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB) disease, which amounts to almost 5,000 deaths each day1. The human microbiome produces metabolites that influence the immune system. Health, therefore, depends on the microbiome, however, the significance of the microbiome in tuberculosis (TB) is just beginning to be understood. Hypothesis: The primary hypothesis of this study is that by conducting microbiome analysis, it is possible to differentiate unique microbial communities found in different disease sites among individuals with pulmonary and extrapulmonary tuberculosis, and this can establish relationships between specific microbial taxa and clinical markers such as CRP levels. Aims and objectives: This study aimed to analyze the microbiome and predicted metagenome of individuals examined for pulmonary or extrapulmonary tuberculosis in an area with a high prevalence of HIV. The goal was to understand the microbial composition and its links to clinical characteristics in this population. Methods (Chapters 2-5): We leveraged ongoing diagnostic trials involving individuals with different forms of TB to characterise the microbiome before treatment. A range of samples were collected (i.e., cough aerosols, oral washes, induced sputum, bronchoalveolar lavage fluid, stool, site-of-disease fluids) from presumptive pulmonary TB or extrapulmonary TB (EPTB) people. Background DNA sampling controls (i.e., saline flush of medical apparatus) were additionally collected, where appropriate. Microbial DNA underwent 16S rRNA gene sequencing and was analysed, and functional metagenomes were inferred. The microbiomes of people with confirmed TB were compared to symptomatic, whilst accounting for clinical factors such as HIV status. Results (Chapters 2-5): In Chapter 2, we show (using a FDA-approved commercial device, PneumoniaCheck) that cough aerosols from people with pulmonary TB 1) contain detectable microbial readouts, including mycobacterial readouts, 2) Mycobacterium tuberculosis complex (MTBC) is detectable by Xpert MTB/RIF Ultra in cough aerosols, and 3) microbiota present in cough aerosols are distinct from those in the upper and lower airways. As TB lymphadenitis (TBL) is the most common form of EPTB, chapter 3 describes the site-of-disease lymph microbiome in people with presumptive TBL compared to symptomatic controls. Briefly, this includes the existence of distinct microbial community states termed ‘lymphotypes’ in definite TBs, and include: "Prevotella-Corynebacterium," "Prevotella-Streptococcus," and "Mycobacterium." The Mycobacterium lymphotype was associated with more severe disease, suggesting disease progression from Prevotella-Corynebacterium and Prevotella-Streptococcus states. The co-occurrence of Corynebacterium and Streptococcus species contributes to TBL pathology. Furthermore, definite TBs were enriched in microbial metabolic pathways related to fatty acids, amino acids, and short-chain fatty acids (SCFAs). These pathways have known proinflammatory immunomodulatory effects that inhibit TB control, and the Mycobacterium lymphotype showed the highest enrichment in these pathways. Chapter 4 describes the site-of-disease microbiome in people with presumptive tuberculous pericarditis (TBP) as it is the deadliest manifestation of EPTB, compared to symptomatic controls. The pericardial fluid (PF) of individuals with TBP differs from those without TBP in terms of both the microbial diversity and the relative abundance of specific taxa (not only Mycobacterium but also other genera like Lacticigenium, Kocuria, and Weeksella). We noted that HIV infection is associated with differences in the abundance of Mycobacterium in PF. Additionally, within individuals with both HIV and TBP (dTBs), the presence of Bifidobacterium is associated with more severe disease, indicated by HIV-positivity and lack of antiretroviral therapy (ART). PF microbial differences between people with definite TB (dTBs) and people without TB (nTBs) are accompanied by variations in functional capacities. Notably, dTBs show an enrichment of pathways involved in SCFA production. Moreover, PF microbiome is linked to distinct clinical and chest imaging characteristics. In Chapter 5, we evaluate the relationship between CRP, the microbiome, and TB by looking at how microbiome members in presumptive EPTB correlate with CRP, as a surrogate for inflammation. We, thus, sought to relate the microbial differences in EPTB to inflammation, represented by levels of the inflammatory marker C-reactive protein (CRP), using site-of-disease samples from our study. In people with presumptive tuberculous lymphadenitis (TBL), those with TB or HIV displayed higher CRP levels, suggesting an interplay between microbial diversity and inflammation. Mycobacterium relative abundance was found to positively correlate with CRP levels, especially in certain lymphotypes. These associations were not observed in individuals with presumptive tuberculous pericarditis (TBP), indicating distinct microbial influences between different TB manifestations. Discussion and conclusion (Chapter 7): In conclusion, this study aimed to improve our understanding of the microbiome's association with TB, especially in vulnerable subpopulations such as HIV-positive individuals. It sheds light on various aspects of the microbiome's association with TB, highlighting how the site-of-disease microbiomes are altered in TB and how specific microbial taxa and metabolic pathways may influence TB pathogenesis and severity. Elevated CRP levels correlated with certain lymphotypes in TBL, indicating distinct microbial influences between manifestations. This study establishes a basis for future research into the microbiome as a potential diagnostic or prognostic marker for TB, a disease that continues to pose a major global health threat.