Cleaning skin and shorts well
A lot of the posts have good advice. One specific solution I found to a similar problem, was to use a gentle, but good quality antibacterial cleanser on my skin and shorts when I started having saddle sores, to disinfect my skin, but also the shorts. If I develop saddle sores, I start using Hibiclens which is an effective but fairly gentle antibacterial cleanser commonly found in physicians offices for hand washing. I keep a bottle in the shower, and wash my nether regions with it after every ride (if I have saddle sores). I also wash the Chamois pad in my shorts with it to disinfect them as well. Also, if you can, lay your shorts inside out, out in the sun to dry, or after they are dry, with the chamois pad getting good direct sunlight. The UV from the sun is good to kill bacteria as well. I like Hibiclens the best, you can find it at many pharmacies, but my back up to that is Phisoderm. I hope that helps.