We are an paperboard packaging manufacturer also. We did a swab several years ago on our equipment and raw materials, the first ever in our plant. Most of the swabs came back negative for any of the microorganisms you listed above. The ones that did show up were only a couple of PPM. After an extensive RA, we determined that, if a building that was nearly 90 years old, machinery that varied between 30 years and 2 years old, and several other surfaces and materials came back either negative or almost too low to measure for any microorganisms, there was a very low likelihood of the contamination from normal operations in the future. At the time (again, 9 years or so ago), we had the information and findings reviewed by the (SQF) technical director and he concurred granting an exemption. A couple of years later, we were told to show the findings to the auditor and he would make the determination if it was still valid. I review the RA annually and verify nothing has changed that could potentially introduce micros into our processes or products. We only did the one swabbing exercise. There are no inherent pathogens in paperboard which undergoes a kill step during manufacturing - steam / high heat. Our adhesives are all certified pure and as a result of chain of custody, all raw materials are delivered door to door. Incoming inspections ensure nothing contaminates our raw materials.
I have the original study, references, and submission to SQF if you're interested, just PM me