by Oliver Yu
In the perfect world, there are no bioreactor or fermentor contaminations.
But if you were to have contaminations, the next best thing would to omnisciently know exactly what the true root cause is.
Since omniscience is not an option here, the next best thing is to narrow down the list of sterile-envelope manipulating actions on the contaminated bioreactor and perform root cause analysis to come up with MPC (most probable cause).
There are a lot of parallels between a crime scene investigation and bioreactor decontamination response. Just as crime-scene investigators attempt to determine the time of death to rule out potential causes outside the time frame, it is a good idea to compute a contamination time-window to rule in/out potential causes.
There are several assumptions in the contamination time-window calculation and which assumptions you use depends on your organization's risk profile. As in, which is worse?
- Coming up with too narrow a time window and risk eliminating the true root cause
- Coming up with too wide a time window and having too many potential causes to investigate?
Step 1: Collect sterility samples and send samples to QC Micro.
Step 2: Get 2 pieces of information from QC Micro:
- Concentration of contaminants in last sample (X)
- Timestamp of last clean sample. (t0)
Step 3: Pick an X0 and try to compute μ.
X = X0 eμ(t - t0)bold is known.
blue is estimated.
red is what you're trying to determine.
The rational number to input here is the limit of detection of your sampling method. If you're going for a narrower window, pick a higher number.
Now you have an estimated growth rate (μ) of the contaminant.
Step 4: Now try to determine the earliest insult (t0)
Again, bold is known; blue is estimated; and red is what you're trying to determine. Here, the key is to guess the concentration of the initial insult. If you're afraid of ruling out the true root cause, pick 1 CFU. If you're going after a realistic time frame to reduce scope, pick what you think a small bolus of contaminants would contain.X = X0 eμ(t - t0)
When you've solved for t0, the second time, you now have computed the earliest time of contamination.
As you can see from this process, there are some serious assumptions. But if applied correctly, you have a scientific and defensible basis for narrowing down potential bioreactor contamination causes and focusing your limited resources on rooting out the most probable cause.
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