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.