I have a client who manufactures a sterile, class III device. The Notified Body does two separate audits -- one for ISO 13485 and one microbiological audit.
The micro audits are done on a regularly-scheduled basis, but less frequently than the ISO 13485 surveillance audits.
I don't see why the two audits could not be done at the same time, except for the difficulty in coordinating the schedules of the two individual auditors.