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The whole EC GMP issue is confusing and many times it is confusing to the inspectorate. This is due to some unfortunate wording being chosen when the September 2003 was written. I will try to answer your question as easily as I can.
a1 Use a particle counter.
a2 Where there is a high risk, monitor continuously.
a3 For routine testing (certification) take a m3 of sample.
So the table is for certification purposes only, what then do we do about monitoring limits.
For 5.0 um this changes, the frequency of alarm is so low that a 95th percentile would run at 0.2 counts which is impossible to manage in real time, so we must now look at the frequency of events not the value of those events. Say for instance your process runs with 5-10 individual counts throughout a 30 minute interval; this is normal for your process, they occur randomly and cannot be attributed to any occurrence in the room, and product continuously meets the sterility tests. So the alarm limit for that process for 5.0um particles would be alarm if you see 3 events in 10 minutes, and alert if you see 2 events in 10 minutes. The value for these events are in m3 and so would read 35counts/m3; this is okay and is normalization, the key is the number of events not the magnitude of such event. If then the system starts to run not at 5-10 but at 10-12 then this increase in random background counts will be annunciated through the alarm system, as it would yield a rate of grater than 2 (or 3) events per 10 minute period. This also allows you to respond to these events in a timely manner.
This is just an outline, but hopefully the same rationale you apply to managing any process variable is applied to the particle counts in the cleanroom.
For more information read our paper Particle Monitoring Requirements in Pharmaceutical Cleanrooms.