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This article explains how to use the Wisconsin Protocol for cleaning air conditioners & heat pumps to avoid Legionella bacteria in air conditioners, how to clean air conditioning systems, Legionnaire's disease prevention & cleaning suggestions for air conditioning equipment and condensate trays, including condensate piping, traps, drains, condensate pumps, and concerns for mold, Legionella bacteria, and other hazards associated with air conditioning systems, cooling towers, and evaporative coolers.
This is a chapter of our full document describing the inspection, maintenance, and repair of residential air conditioning systems (A/C systems) to inform home buyers, owners, and home inspectors of common cooling system defects.
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The Wisconsin protocol for cleaning air conditioning condensate trays includes "This procedure calls for an initial shock treatment with 50 ppm free residual (total) chlorine, addition of detergent to disperse bio-fouling, maintenance of 10 ppm chlorine for 24 hours, and a repeat of the cycle until there is no visual evidence of biofilms. To prevent exposure during cleaning and maintenance, wear proper personal protective equipment: a Tyvek-type suit with a hood, protective gloves, and a properly fitted respirator with a high-efficiency particulate (HEPA) filter or a filter effective at removing one-micron particles."
There is some suggestion that using chlorine products is more likely to damage the equipment by corrosion. For example simply pouring bleach will produce chlorine gas and will corrode nearby aluminum fins on an evaporator or condenser coil. This is a well known problem and there must be a collection of standard products offered to the HVAC industry.
http://www.osha.gov/dts/osta/otm/otm_iii/otm_iii_7.html is OSHA's technical manual re Legionnaire's disease and has some (incomplete) details "disinfecting the cooling tower system according to the Wisconsin Division of Health protocol for "Control of Legionella in Cooling Towers" or a similar process for cleaning heat rejection systems that follows sound practices to minimize potential for Legionella growth."
A section in this document discusses the use of commercial biocides (looks questionable), traditional oxidizing agents (chlorine), or bromine (effective and less corrosive). In the case of Legionella, other measures like temperature control and cleaning frequency are cited as also important.
I would look for a disinfectant that would be broad spectrum but which also is assured not to damage the equipment, maybe a bromine product.
Some history behind the "Wisconsin protocol" for cleaning air conditioning condensate trays may be in order.
By coincidence my associate Craig Balchunas (Poughkeepsie, NY) returned from a one day class on Legionella where he spoke with one of the original contributors to the "Wisconsin Protocol". He informs me that the protocol was an "off the cuff" exercise by a group of professionals in response to an urgent protocol request from the Wisconsin DOH, that the protocol has not been tested scientifically, and that there may be problems with corrosion damage to equipment when the protocol is followed.
Therefore we add that for any disinfection using corrosives (as I anticipated in my comment below) since there is risk of damage to the equipment, you'll need to wash the disinfectant off thoroughly at the end of the procedure.
We also discussed UV lights as a disinfection method - a method I view with skepticism for several reasons including questions about adequacy of exposure time in air systems and similarly, because some pathogens find intermediate hosts (such as Legionella bacteria hiding in an amoeba) which protect them as they pass through the UV system.
At the end of the day, regular inspection and cleaning and control of blow-by of unwanted condensate droplets are what make the most sense to me.
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