A friend with who I have done long bike tours was constantly getting sores but I have never had a problem. The difference is that I wear jocky shorts and put on a clean pair under my bike shorts at the start of the day. No chance for bacteria to build up and cause an infection. The cotton jocky shorts get washed in a mild bleach solution that is going to disable any bacteria.
One could spray a disinfectant on the padding for the bike shorts but most of them contain chemicals that are absorbed through the skin and at the very least can cause a rash.