If you want to limit or control bacteria in your HVAC, make sure you use fresh air mode as much as possible not recirc, and also turn off the A/C about 1 minute before turning the RAV4 off and let the fan run full blast(its easier when you know ahead of time). This will dry out the ducts and ensure there is no moisture to grow bacteria or anything else.
I always do this when I know I will be stopping and I have never had a problem with any smell or bacteria in any car I have owned.
Its hard to do if its blistering hot outside, just roll the windows down a bit and with the fan running full blast, the ducts are still cool enough to keep you from melting.
For those who live in an area where the air outside is dirty, bad whatever, just make sure you have a good cabin filter. I make my own using hammock filters for furnaces(comes in a blanket which is easy to cut). It is MERV 11 and it captures dust, bacteria, pollen, smog etc. It captures enough particles for me. With the toyota basic filter I can smell the dust(you know the smell when running through a dirt road) and I see "stuff" blowing from the vents. With my own filter I see nothing nor do I smell the majority of things including some smoke. There is also no reduction in air passing through the filter(as long as I change it regularly).
I can post a set of pictures for those who want to know how I do it. Basically I can make about 20 filters with one package that I buy for 8.99(roughly $0.50 each) Since I install them flat I have to change them every 15 days but its a lot cheaper than buying a toyota cabin filter(cost $16). Costs me about $12 annually as opposed to over $70 with the toyota(I had to change them every two months)
Cheers