“Genetic diversity of Mycobacterium tuberculosis complex in treatment naive sputum smear positive patients as revealed by spoligotyping and MIRU-VNTR.”

PURPOSE: The molecular epidemiological methods are important in the study of transmission dynamics and population structure of Mycobacterium tuberculosis strains circulating in a geographical region. METHODS: A total of 104 patients were selected who were diagnosed for the first time with pulmonary tuberculosis and were sputum smear positive. Drug sensitivity test, spoligotyping, and MIRU-VNTR typing were done with all strains. RESULTS: In our series, three isolates were resistant to all the four agents, while 13(12.5 %) were classified as multi-drug resistant. Spoligotyping revealed the predominance of East African-India (EAI) lineage (66.3 %) with EAI 3-Ind (44.2 %) and EAI 5 (18.2 %) making up the majority. Our study found no presence of Beijing strains, while 15 isolates exhibited 9 distinct spoligotyping patterns (orphan or novel) that are not listed in the spoligotyping database. Three strains belonging to CAS1-Delhi, EAI3-Ind, and Manu1 lineages were resistant to all four anti-tuberculosis agents. The discriminatory power of various MIRU-VNTR alleles was found to be lower for EAI family strains compared to Non-EAI family strains. The clustering rates of MIRU-VNTR and Spoligotyping were 0.52 and 0.711 respectively. The neighbor-joining tree, based on 24-loci MIRU-VNTR typing, revealed two main clusters: one group included the CAS1-Delhi, LAM6, Cameroon, and MANU families, while the other group contained the EAI family. CONCLUSIONS: The finding of half of the strains resistant to one or more anti-tuberculosis drugs and 12.5 % MDR strains emphasizes the importance of susceptibility testing before initiation of treatment.EAI lineage is considered to be predominant in Southern part of India which was corroborated in our study. MIRU-VNTR should be used in addition to spoligotyping since it has got finer discriminatory power. Molecular epidemiological studies should be performed periodically to assess the circulating strains in a particular geographic area.