Molecular epidemiology of Mycobacterium tuberculosis isolates from Kerala, India using IS6110-RFLP, spoligotyping and MIRU-VNTRs

► High prevalence of zero-copy and single copy IS6110 isolates from Kerala. ► MIRU-VNTR showed better discrimination than IS6110-RFLP and spoligotyping. ► EAI/Indo-Oceanic lineage M. tuberculosis strains are prevalent in Kerala (71%). ► Combination of Spoligotyping with MIRU-VNTRs is optimal for molecular epidemiology. Tuberculosis (TB) continues to be a major health problem in India, and there is very little information about the prevalent genotypes of tubercle bacilli that cause TB in India, especially in Kerala. Our aim was to study the different circulating strains of Mycobacterium tuberculosis (MTB) that are prevalent in Kerala, India. We analyzed 168 MTB isolates from as many pulmonary TB patients using IS6110-RFLP, spoligotyping and MIRU-VNTRs. The results of IS6110-RFLP revealed that majority of isolates had null copy (10.89%) or single copy (44.87%) of IS6110 insertion. Low copy (