Bacterial Genotyping of Central Nervous System Tuberculosis in South Africa: Heterogenic Mycobacterium tuberculosis Infection and Predominance of Lineage 4

Abstract

Tuberculous meningitis (TBM), the most severe extrapulmonary manifestation of tuberculosis, is caused by the pathogen Mycobacterium tuberculosis. The M. tuberculosis complex includes seven lineages, all described to harbor a unique geographical dissemination pattern and clinical presentation. 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 neuropathological 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. Of the 83 patient specimens tested, bacterial characterization could be performed on 46 specimens (55%). M. tuberculosis lineage 4 was present in 26 patient specimens (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. 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 harbor more than one M. tuberculosis lineage in the CNS.

Central nervous system tuberculosis

“…The genetic diversity of Mycobacterium tuberculosis lineage affects the disease phenotype, including the virulence, transmission, reactivation, reinfection and treatment response. Euro-American lineage was found predominantly in 83 TBM patients in South Africa; lineage mixed infections detected in those samples indicating the rapid progression of the disease and inadequate response therapy [11].…”

“…The genetic diversity of Mycobacterium tuberculosis lineage affects the disease phenotype, including the virulence, transmission, reactivation, reinfection and treatment response. Euro-American lineage was found predominantly in 83 TBM patients in South Africa; lineage mixed infections detected in those samples indicating the rapid progression of the disease and inadequate response therapy [11]. ] confirmed the overall estimates of commercial nucleic acid amplification (NAA) sensitivity and specificity of 82% (95% CI 75-87) and 99% (95% CI 98-99), respectively, against combined reference standard (CRS) (clinical criteria and one or more of the followings: Ziehl Neelsen, culture or CSF-positive NAA test.…”

Genomic characteristics of prospectively sequenced Mycobacterium tuberculosis from respiratory and non-respiratory sources

“…M. tuberculosis isolation from a non-respiratory source, such as lymph node biopsies, pleural fluid, cerebrospinal fluid, and various other tissues reflect EPTB, 2 although PTB and EPTB may be present at the same time, in which case, it is programmatically classified as PTB—by convention. The demographic characteristics of patients with PTB and EPTB have been explored in multiple studies, 3 , 4 , 5 but few studies were able to reflect on genomic differences between strains causing PTB and EPTB disease, 6 , 7 , 8 and none have been able to do it in a comprehensive prospective fashion. The implementation of routine whole genome sequencing allows comprehensive genomic characterization of M. tuberculosis strains, including lineage/sub-lineage assignment, mixed strain population (simultaneous co-infection with more than one strain), drug resistance, and transmission cluster identification.…”