Molecular genotypes of Mycobacterium tuberculosis strains circulating in Dakar, Senegal

Tuberculosis is a contagious infectious disease, in which epidemiologic monitoring by molecular approaches is a critical element of prevention and control. The population structure of the Mycobacterium tuberculosis complex (MTBc) in Senegal was last described in the 1970’s using biochemical methods. In this present study, we applied molecular approaches to genotype M. tuberculosis isolates from active pulmonary tuberculosis patients who participated in a prospective cohort study between 2004 to 2006. Genetic characterization, using standard spoligotype analysis and Line Probe Assay for resistance to isoniazid and rifampicin, was applied after culture on egg based solid media. The prevalence of resistance to isoniazid was 1.0% and to rifampicin 0.0% among 203 isolates tested. Of the 203 isolates, spoligotype patterns present in the TB-insight database were identified in 178 (87.6%) while 25 (12.3%) showed patterns suggestive of mixed infection. The major spoligotypes identified were the Haarlem lineage (22%), followed by the T (19%), Beijing (12%), LAM (12%), and M. africanum West African 2 (10%). Patterns suggestive of mixed infections, such as the sole lack of spacers 33 and 34, suggested a combination of Euro-American M. tuberculosis and Beijing lineage, which were confirmed by polymerase chain reactions (PCRs) for lineage defining deletions in a subset of isolates. The population structure of the M. tuberculosis complex in Dakar reflects a predominance of Euro-American M. tuberculosis (Haarlem, T and LAM), with a decreased prevalence of M. africanum West African 2, compared with reports from the 1970’s based on biochemical speciation, which reported prevalence of M. africanum around 20% in Dakar.