Molecular Epidemiology of Mycobacterium Tuberculosis Complex in Ghana: Understanding Transmission Dynamics

Abstract

Tuberculosis (TB), a disease of antiquity, still infects millions of people annually. In 1993 the World Health Organization declared it a global health emergency, calling for more resources and studies to aid control this global menace. An objective under the research pillar of the End TB Strategy, is to investigate the transmission dynamics of the disease using molecular epidemiology (molepi) to understand factors leading to occurrence of the disease within distinct populations. Consequently, this PhD work sought to use a population-based molepi study to determine the transmission pattern and dynamics of Mycobacterium tuberculosis complex (MTBC) strains from two areas in Ghana (East Mamprusi and Accra Metropolitan Area) and identify associated risk factors to complement conventional control program efforts. Mycobacterial species isolated from consecutively sampled pulmonary TB patients presenting at 13 selected health facilities between July 2012 and December 2015 were confirmed as MTBC by IS6110 and rpoß PCR and further assigned lineages and sublineages by spoligotyping and large sequence polymorphism PCR assays. Patient characteristics were obtained with a structured questionnaire. We used SaTScan and ArcMap analyses to identify and map significantly clustered MTBC lineages/sub-lineages. Isolates were strain typed using standard mycobacterial interspersed repetitive-unit variable-number tandem repeat (MIRU-VNTR) typing. Whole genome sequencing (WGS) was performed to resolve traditional genotype clusters and epidemiologically linked cases. Phylogenetic analysis was then used to assess strain relatedness. Among 2,551 isolates genotyped for spatio-temporal analysis, 2,019 (79.1%), 516 (20.2%) and 16 (0.6%) were identified as M. tuberculosis sensu stricto (MTBss), M. africanum (MAF) and animal strains respectively. MAF lineages were found to persist at approximately 20% over an 8-year period. Whereas the Cameroon sub-lineage was associated with Southern Ghana, the Beijing, Ghana and animal genotypes were significantly (p<0.05) associated with Northern Ghana. We estimated recent transmission rate of 24.7% using WGS and confirmed the existence of reduced recent transmission of MAF compared to MTBss L4. WGS confirmed a wide spread of a Cameroon sub-lineage clone mainly from the Ablekuma sub-district. More importantly, we identified a recent transmission cluster associated with isoniazid resistance belonging to the Ghana sublineage of L4. Risk factor analysis using logistic regression modeling, identified younger individuals (age <30 years) and male gender as significant risk factors for recent TB transmission. Majority (94.4%, 34/36) of individuals with recurring TB episodes were males and 58.6% (21/36) had TB recurrence within 12 months post treatment. Recurrent TB was attributed to inadequate treatment (relapse of same strain) in 75.0% (27/36) of participants with 25.0% (9/36) attributed to re-infection. Epidemiologically linked TB cases were likely the results of recent TB transmission within the house or from neighboring recent transmission events. For the first time in Ghana using WGS, we confirm high recent TB transmission within the population driven largely by MTBss sub-lineages Cameroon and Ghana and show that unresolved previous infection due to inadequate treatment is largely the cause of recurring pulmonary TB. Observed reduced recent transmission of MAF suggests other factor(s) (host/environmental) may be responsible for its continuous presence in West Africa. We show that it is possible to monitor recurring TB cases and follow-up household related transmission in a resource-limited setting.