Background: Tuberculous meningitis (TBM), the most severe extra-pulmonary manifestation of tuberculosis, is caused by the pathogen Mycobacterium tuberculosis. The M. tuberculosis complex includes seven lineages, all described to harbour a unique geographical dissemination pattern and clinical presentation.

Method: In this study, we set out to determine whether a certain M. tuberculosis lineage demonstrated tropism to cause TBM in patients from Cape Town, South Africa. DNA was extracted from formalin-fixed paraffin embedded central nervous system (CNS) tissue from a unique neuro-pathological cohort of 83 TBM patients, collected between 1975 and 2012. M. tuberculosis lineages 1, 2, 3 and 4 were determined using an allele specific PCR and Sanger sequencing.

Results: Of the 83 patient specimen tested, bacterial characterization could be performed on 46 patients (55%). M. tuberculosis lineage 4 was present in 26 patients (56%) and non-lineage 4 was identified in 10 cases (22%). Moreover, genomic heterogeneity was detected in the CNS specimens of 7 adults and 3 children.

Conclusion: We could show that infection of the CNS is not restricted to a single M. tuberculosis lineage and that even young children with rapid progression of disease can harbour more than one M. tuberculosis lineage in the CNS.