Genotypic and epidemiological characterization of Mycobacterium tuberculosis complex in Ghana

Tuberculosis (TB) remains a public health challenge. In 2013, TB was estimated to have caused 9 million incident cases of which 1.1 million were co infected with HIV and 1.5 million deaths worldwide. For the effective control of TB, the use of simplified diagnostic tools for case detection diagnosis of drug resistant TB and understanding the effects of comorbidities such as HIV on the prevalence of TB is paramount. Ghana, housing six of the seven phylogenetic lineages of Mycobacterium tuberculosis complex (MTBC) with high TB/HIV prevalence provides a unique opportunity to study and better understand the dynamics of TB.
In the context of TB control, we studied the level of drug resistance using phenotypic drug susceptibility testing (DST) and correlated the DST results with patient treatment outcome (Chapter 3). We found a low rate of multidrug-resistant (MDR)-TB rate (1.9%), high isoniazid (INH) mono resistance (15%) and the dependence of treatment outcome on the susceptibility to rifampicin (RIF). For the rapid diagnosis of MDR cases, we further evaluated the accuracy of a molecular base diagnostic tool (Genotype MTBDRplus) and compared it with the gold standard phenotypic DST method (Chapter4). We found 100% correlation for detection of both MDR and RIF mono resistance and 83% for INH mono resistance. The remaining 17% INH resistance detected by standard phenotypic DST but not Genotype MTBDRplus are likely due to molecular mechanisms whose targets are not interrogated by Genotype MTBDRplus. The high overall sensitivity and the relative short turn- around time of Genotype MTBDRplus makes it a valuable addition to diagnostic algorithm in Ghana.
The control of TB also depends on understanding the patterns and dynamics of TB transmission to reduce source of infection. Existing tools for studying transmission such as MIRU-15 used for routine molecular epidemiological studies have been shown to exhibit varying discriminatory power among the different human-associated MTBC lineages. We established a robust and cost-effective PCR based reduced but lineage-specific set of MIRU-VNTR loci with high discrimination power in the main MTBC circulating in Ghana (Chapter 5). This assay will help identify risk factors that enhance transmission and patient groups at increased risk of developing TB. In addition, this assay can be used to differentiate between exogenous re-infection from true relapse cases
SNP- based genotyping and spoligotyping established that M. africanum (MAF) still causes 20% of all TB cases in Ghana (Chapter 6 and 7). Reasons for the restriction of MAF to West Africa have eluded researchers for many years. Using retrospective isolates, we provide for the first time plausible reason why MAF is restricted to parts of West Africa. We showed a significant association between MAF and the Ewe ethnic group. This association was confirmed using prospective isolates and supports possible host pathogen co-evolution inn TB. In addition, we observed a strong association between MAF2 and HIV co-infection supporting the notion that MAF might have a lower virulence compared to other MTBC in humans