The microbiome and Tuberculosis - filling the gaps

Abstract

Globally tuberculosis remains one of the leading causes of mortality from any infectious agent. Evidence has shown that there are links between TB and the human microbiome and that alterations to the host micro flora in response to TB infection and subsequent treatment may have a powerful impact on both treatment outcome and patient health. Research regrading several factors surrounding TB and the microbiome, for example the resistome require urgent attention. Along with this there is also a constant need for new methods to study TB and the microbiome as the research field progresses. The first objective of this study was to determine the suitability of DNA extracted by means of the NWU lysis method for bacterial microbiome analysis; and amplicon-based next generation sequencing (NGS) in comparison to DNA obtained by various commercial kits; and the second objective was to examine changes in the bacterial microbiome of the respiratory tract during the process of TB therapy over time in human participants (sputum) by whole genome shotgun sequencing in comparison to the respiratory microbiomes of healthy controls. Applying the NWU lysis method to a mock microbial community, did not reveal any conclusive results. Following analyses on more complex samples revealed that the NWU lysis method has potential for downstream microbiome analyses but further optimisation will be required. The second objective was to examine changes in the respiratory tract microbiome during the process of TB therapy over time in the sputum human participants. Results revealed significant changes in both taxonomic composition and within the associated resistome. Overall microbiome diversity was increased in response to treatment, suggesting that microbial perturbation in response to treatment may give foreign or less abundant, potentially more resilient bacteria a chance to proliferate. Results also revealed a increase in the presence of acquired aminoglycoside resistance genes (aadA, aadE, aac(2')-I, aph(3')-I, aph(3'')-I, aph(3''')-III, and aph(6)-I) linked with patient samples. The results obtained could thus be a cause for concern, especially considering the high prevalence of HIV/AIDS amongst individuals infected with TB, but further studies will be required to determine if there is any physiological or clinical significance to these observations.