Molecular diagnosis, genetic diversity and drug sensitivity patterns of Mycobacterium tuberculosis strains isolated from tuberculous meningitis patients at a tertiary care hospital in South India

Abstract

Tuberculous meningitis (TBM) is the most severe form of Mycobacterium tuberculosis (Mtb) infection in humans and is a public health concern worldwide. We evaluated the performance of GeneXpert MTB/RIF (GeneXpert) for the diagnosis of TBM. In addition, genetic diversity and drug susceptibility profiling of Mtb strains isolated from TBM patients were also investigated. A total of 293 TBM suspected cerebrospinal fluid (CSF) samples were collected and subjected to GeneXpert and Mycobacterial Growth Indicator Tube (MGIT 960) culture, respectively. Sensitivity and specificity of GeneXpert was 72.7% and 98.5%, respectively by using MGIT 960 as a gold standard (GeneXpert (n = 20, 6.8%) vs MGIT 960 (n = 22, 7.5%)). All Mtb positive cultures were subjected to 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) typing, Line probe assay (LPA) and MGIT 960-Drug Susceptibility Testing (DST). The rpoB gene was amplified and sequenced for selected isolates. Among our TBM patients, East African Indian (EAI) lineage (n = 16, 72.7%) was most predominant followed by Beijing (n = 3, 13.6%), Sfamily (n = 2, 9.1%) and Delhi/CAS (n = 1, 4.5%). Three Mtb strains were found to be Isoniazid (INH) resistant by MGIT 960; however LPA revealed that two strains were INH resistant and one strain was multi drug resistant (MDR) (Resistant to Isoniazid and Rifampicin (RIF)). We identified rifampicin resistant isolate with the mutation D516F in rifampicin resistancedetermining region (RRDR) and observed discordant results between LPA, GeneXpert and MGIT 960. In addition, GeneXpert showing false RIF resistance was identified (no mutation in RRDR). We conclude that GeneXpert is useful for the diagnostic confirmation of TBM; however a GeneXpert negative sample should be subjected to MGIT 960 culture or LPA to rule out TBM. EAI lineage was the most predominant among TBM patients in South India and associated with drug resistance. The discordance between GeneXpert, MGIT 960 and

Epidemiology of Mycobacterium tuberculosis lineages and strain clustering within urban and peri-urban settings in Ethiopia

“…In this regard, the findings observed in this study seem to agree with others that suggested a possible relationship between L3 and EPTB disease [ 12 , 38 ] . Correspondingly, a significantly higher rate of PTB was often associated with L4, while more EPTB disease, such as TB meningitis and TBLN, was attributed to L3 [ 13 , 15 , 38 ] .…”

“…Although, it is still challenging to investigate the influence of bacterial and host genotype on the development of different forms of TB in humans, disease phenotype seems to be associated with a bacterial genotype [2,6]. According to other published reports, L4 seemed more likely to be associated with Pulmonary TB (PTB) while L2 and L3 were linked with extra-pulmonary TB (EPTB) disease, such as TB meningitis and TB in cervical Lymph Nodes (TBLN) [12][13][14][15]. Another comparative study showed that strains of the East African Indian (L3) and Euro-American (L4) lineages were negatively associated with extra thoracic disease as compared to strains of the East Asian lineage (L2) [16].…”

Five Priorities of African Genomics Research: The Next Frontier

“…Thus, the pharmacogenomics of infectious diseases (e.g., AIDS, tuberculosis, malaria, and COVID-19) is important for African populations, while the pharmacogenomics of cardiovascular diseases is becoming important, as is the case for cancer and hypertension. Several studies have shown resistance due to genetic variations in two of the most expanded infectious diseases in Africa, AIDS (91) and tuberculosis (34,58,107).…”