Hello JR,
Does your facility follow any specific Food Safety certification? I'm not familiar with ISO, BRC, or FSSC guidelines, but I know that SQF has some guidance on air quality. It's reads as though compressed air that touches food or food contact surfaces is the main concern, but I've had auditors state that they're just as concerned with the filtration systems for ambient air.
Here is what's stated in regards to air quality the SQF Edition 8.2 Auditing Guidance document, under Module 11.5.5 The Quality of Air and Other Gases:
"The site may consider the following controls for particulates
i. Intake filters to remove atmospheric dirt and solid particulates.
ii. Microorganisms – A point-of-use filter, minimum 0.01 micron, prevent pathogenic microorganisms from contaminating food. An effective PM program should be in place to maintain the integrity of the filter. Validation from the filter manufacturer is often considered adequate validation."
Overall, your needs would really depend on the type(s) of contamination you're trying to protect against. What type(s) of microbial contamination are your products most at risk for? Are there any physical or chemical hazards that would need to be addressed with the filtration? I would recommend doing a risk assessment with some other team members and discussing your concerns. At my facility, we perform ambient air testing annually to check for spoilage organisms (yeast & mold), and the air handling systems at my facility (both ambient AND compressed) have filtration down to 0.01 microns, to help mitigate any microbial contamination. As recommended above, have your maintenance staff include checking the filters on a designated schedule as a preventive maintenance step - with a high level of filtration, those filters clog up at a faster rate than standard filters.
Hope this helps,
Chrispy Chips