However, whether or not to use "bugs" here depends on how formal or informal you are being. Since it sounds like informal writing, it is appropriate. This is particularly true since in informal writing we call resistant bacterial "superbugs."
"Bug" means "any disease-causing microorganism" and thus includes both bacteria and viruses. Antibiotics, of course, only affect the larger microorganisms like bacteria and spirochaetes, and don't affect viruses.