Which method you are using for DNA extractionm

The CTAB method seems to give good results.

I agreed with M N Manoj. I have used the below method. It works well

Two to three loop full of mycobacterial cultures were suspended in Tris-EDTA buffer (pH 8.0). Each cell-suspension was used for DNA extraction by enzymatic method with lysozyme and then purified with CTAB/NaCl and chloroform/isoamyl alcohol.

Try to read this review, it may helpful for you.

Best 

If you need a good concentration of DNA you should culture MTB isolates on L-j medium. After obtaining sufficient growth you can take loopfull of colonies and can proceed for DNA -isolation either by chloroform isoamyl alcohol method or by sonication method. This way you can get good yield of DNA. If you need protocol of CI   method let me know will be glad to share.