Genotyping Mycobacterium tuberculosis isolates with few copies of IS6110: Value of additional genetic markers

•IS6110 RFLP is the best typing method for Mycobacterium tuberculosis.•Strains with fewer IS6110 copies needs sensitive method for typing.•Discriminatory power of spoligotyping was higher than IS6110-RFLP in isolates with single copies of IS6110-RFLP.•Authors propose combination of FAFLP and Spoligotyping for M. tuberculosis strains harboring few copies of IS6110.