I would use set test tube culture with gental.daily swirl. Allow clumps to settle and single cells to float around. OD optical density was used to set cultures to grow for infections of moi 1:1 , from very dilute cultures to infecet. i was fortunat, i cloned gfp into h37rv and was able to see single cells via bacteria hawksley counting chamber under oil without having to do an acidfast stain.
Seemed the more i used physical force to get single cells, vortex, sonicate, shake, the more it would clump. Like the shearing of thr fine sugar like biofilm the more clumping that happen. It grows budding like so clumping is its naturally happy place.
I was wantting to try a sires of filtration gently done step wise from high to low...? I never did, but the daily gentle swirl if set culture with lose cap or cotten ball will work well.