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Most closed circuits are used to conduct heat either to warm up a process or property or to cool it down such as in refrigeration/air conditioning.
The water in these systems is susceptible to microbiological contamination, scale & corrosion and any one of these can cause efficiency to drop.
When it comes to bacteria, there are some such as Pseudomonas which form a slime which can block heat exchangers. Whilst others, such as Sulphate and Nitrite reducers cause chemical reactions in the water which encourage corrosion.
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When taking a sample from a drain point, thoroughly clean and sanitise it first.
Next, flush a few litres to waste before filling the sample bottle.