Maybe a few questions first. Bare with me, they may seem obvious or irrelevant to you but it will help narrow down the problem. Please don't get offended.
*Are you sure it is a bacterial infection? Can you accurately identify good/bad bacteria?
*Is the environment that you work in free of drafts, moldy air, airborne dust or flour?
*Is EVERYTHING (including hands, spoons, thermometers) sanitized?
*How long are sanitized items and areas left exposed to open air?
*Have you watched more than one video about proper sanitation?
*If you rinse after cleaning, is your tap water free of bacteria? Try no-rinse, Star-san?
*Are there people, children or pets that may be getting in or around your stuff?
Shooting from the hip I would ask this: Is it within your budget to just toss anything suspicious and start over with new equipment? (Plastics can be hard to sanitize in some cases)