Okay! I know this one! You need an "Environmental Monitoring Program"
Pathogens you test for will be pathogens you are at high risk for. So for me in chocolate, we monitor for Salmonella. I don't know anything about bakeries, but if you look for recalls, you will find the most common pathogens. What you're trying to do is identify a problem before it gets to your product zone / food contact surface. If I find Salmonella in a drain, I know someone washed equipment with Salmonella on it. And then I go Salmonella hunting.
You want to test according to risk - so if you're truly low risk, you shouldn't have to test very often. Take a large initial swab set of door ways, drains, anywhere high traffic or wet/warm, equipment stands & sides, crevices, along pipes, etc. If you don't find anything taking up house, hooray! Set it to monthly . If you go a few months without a hit, set it to quarterly. If you find something, you have to swab more frequently. I've never found anything in my plant, but I swab biweekly. I started with weekly swabs but the risk/time/cost math didn't add up. Always send to a certified lab.
You're going to want to think in zones - zone 1, food contact surface, zone 2 next to a food contact surface, zone 3 gross stuff in the factory, zone 4 outside of the factory.
Never swab zone 1 for pathogens. If you get a positive on a food contact surface, that's trouble. Instead swab for indicator organisms, like e bac.
Swab zone 2 a lot, and zone 3 drains and floor scrubbers like all the time.
You need to also set a corrective action for if you do find a positive. How to clean, what the corrective action timeline is, etc. For my program we clean and swab on presumptive, divert foot traffic if possible, and initiate a corrective action within 72 hours (fix the leak, clean more frequently, whatever gets rid of it). Then we swab around the area like a 360 spider web - find out where its hiding. Clean hot spots and swab until you get negatives. Some companies dont swab in presumptives, they wait. On one hand, you hope you never have to do this. On the other hand, presumptives are common and I find it gives my staff experience cleaning gross spots and paying attention to micro risk. It's more critical when you're dealing with agricultural / dirty field stuff. If you're confident there are no pathogens, you won't need Plan B.
Get some advice from someone else in baking though, I really don't know a thing about that process.