which guideline or reference state that we have to test for pathogens for swab samples?
No guideline says to do so but it is a common practice in pharmaceutical field.
Pathogens have to test only in raw material and finished product but not in environmental monitoring.
Testing product contact equipment for pathogens is required if you haven’t done cleaning validation or established cleaning verification. There is literature available for equipment cleaning validation and some forums may even provide a template. If you go to EU website and search equipment cleaning , you will get info that will help. I don’t know off hand what the numbers are but will provide update once I look over note from what I did. I do know swabs are used a lot for ball valves and other hard to clean surfaces. Soaking them in a caustic solution and disassembling them will help with cleaning them. Good luck.