Evolutionary history and molecular epidemiology of "Mycobacterium tuberculosis" in Tanzania and across Africa

Abstract

Humans have been affected by tuberculosis (TB) for millennia. Today, TB remains a global health problem and the leading cause of mortality due to a single infectious agent. TB in humans is primarily caused by seven human-adapted phylogenetic lineages of Mycobacterium tuberculosis (Mtb) complex. Mtb lineages differ in their geographical distribution, partly reflecting human demographic histories. Importantly, variation in Mtb is known to impact TB infection and clinical disease. In recent years, advances in sequence-based molecular markers i.e. single nucleotide polymorphisms (SNPs) and whole genome sequencing (WGS) technologies have enabled robust classification of Mtb strains which ultimately have allowed researchers to address important questions regarding Mtb phenotypes, transmission patterns and the evolutionary history of TB. Remarkably, such investigations remain underexplored in high-endemic TB settings of sub-Saharan Africa. By applying phylogenetically robust methods such as SNP-based typing complemented with WGS we can gradually disentangle the role of Mtb variation on TB epidemic in high burden clinical settings. On the other hand, with recent large-scale WGS, it is becoming clear that Mtb strains are heterogeneous at the lineage level. Several studies have explored the phylogenetic substructure of Lineage 2 and Lineage 4; the two most geographically widespread and more successful Mtb lineages. However, Lineage 1 and 3 are still important drivers of TB epidemics along the Indian Ocean rim, which includes parts of Africa. Yet to date, the phylogeographies of these two lineages have not been fully explored. By contrast, Lineage 2–Beijing seems to have emerged only recently in Africa. Among the seven Mtb lineages, Lineage 2–Beijing is highly virulent and associated with antibiotic resistance; thus, this calls for investigation of its origin on the African continent. In this thesis, we aimed to gain countrywide insights into the genetic diversity of Mtb in Tanzania based on SNP-typing. Secondly, using a combination of SNP-typing and WGS techniques we describe the local diversity of Mtb and assessed for clinical phenotypes in urban and rural settings of Tanzania. We then studied the global phylogeographies of Mtb Lineage 1 and 3 to infer their evolutionary histories and global spread. Finally, we analyzed the origin of Mtb Lineage 2–Beijing in Africa using WGS. This thesis contains 7 chapters. The first two chapters provide the background on TB, Mtb lineages, and the objectives of the thesis. The remaining four chapters cover the conducted research performed during this PhD thesis. In the final chapter, we summarize the key findings, limitations and discuss the general implications of our work. In Chapter 1, we highlight the global burden and control of TB, the outcome of TB infection and disease, the overview on the Mtb genetic diversity, different molecular markers and genotyping techniques, and the consequences of Mtb diversity. In Chapter 2 we state the objectives of the thesis. In Chapter 3, we studied a countrywide population structure of Mtb in Tanzania based on SNP-typing and assessed relationships between Mtb lineages with patients’ clinical and sociodemographic characteristics. In Chapter 4, we zoomed into the local urban and rural settings of Temeke, Dar es Salaam and Ifakara, Morogoro in Tanzania, to identify clinically relevant Mtb phenotypes. In addition, we describe the local diversity and performed an exploratory analysis on transmission patterns in the urban setting. In Chapter 5, we studied the phylogeography and the spread of Lineage 1 and 3 using global representative genomes from places where strains of the two lineages are frequent. In Chapter 6, we used whole genome sequences of Mtb Lineage 2–Beijing to investigate the evolutionary history of this lineage in Africa. We reveal multiple introductions of Mtb Lineage 2–Beijing into Africa originating from Asia. We further show that these introductions occurred over the last 300 years, with most pre-dating the antibiotic era. In Chapter 7, we summarize the key findings from this PhD thesis, discuss the implications and highlight future directions.