Considering the scale of IC's using sub 50nm technology, I would think that even thought fabs are incredibly clean, there would still be a substantial amount of bacteria. Do they prove problematic in leaking current/shorting parts of the circuit?
Perhaps the term "particle counter" is what you need. Smaller bacteria are one-micron spheres, and WP gives some fed. standards for various classes of cleanroom:
Parts of fab take place in vacuums way below a micron, where aerosols are impossible. (Bacteria would have to form molecular beams! Or, perhaps bounce in parabolic trajectories, if surface temperatures were high enough.) I'm just speculating. I'd expect that much smaller carbon & salt nanoaerosols, and the purity of wash fluids would be a much bigger issue than keeping bouncing-ball spore particles out of your 0.01 millitorr chambers.
More speculation: bacteria stick to everything, so we wouldn't find them suspended in vac chambers. On the other hand, "weaponized" bacteria are somehow given a coat without ions or dangling bonds, so they behave more like nano-sand. From "Demon in the Fridge" book, they found that an ampuole of weaponized bacteria will "evaporate" to form a cloud of bouncing particles at roughly 100F. They don't look like smoke, more like transparent colored gas.