There are many interesting comments from several informed individuals. The question that has not been answered is how do duct systems get dusty and dirty? As a RESNET Home Energy Rater, I perform pressure tests on homes and duct systems, and the one common thread is . . . most air delivery sytems have large amounts of air leakage. The solution is to seal the duct system, and pay particular attention to the return duct system and ductwork near the air handler (the 'blower'). As others have said, a captive (sealed) duct system with proper filter maintenance should be more then adequate for most occupants. For those who have allergy, asthma, or other breathing problems, a filter with a higher MERV rating (number should be listed on the package) or a HEPA filter are good choices. These filters will capture smaller particulates and should improve the indoor air quality. Again, make certain that the entire duct system is sealed, preferably with mastic, second choice UL-181 foil tape - never use cloth duct (also known as duck) tape.
The short answer is yes, duct cleaning, done right by a reputable company will help with the smell. It is likely though the smell is coming from another source, ie the crawl space. It could also be that another rodent is dead in the duct work. A visual inspection would be in order to check for any breach in the duct system. A duct pressure test would be able to tell you how much air is leaking from the system over all. A hole large enough for an animal to enter would loses a great deal of air, over 300 CFM. It would be worth looking into having this test done and it should cost around $200. Cleaning the air handler and evaporator coil will greatly improve the performance of the air conditioner. Dirt and dust on the evaporator acts as insulation and reduces the amount of cooling done be the coil. Any quality duct cleaning should include cleaning the air handler and coil, and the tech should allow you to watch him perform the work as it is done.
I have been a plumbing/gas/hvac tech for 19 years, before that I installed ductwork in commercial buildings and office towers. As the article states, unless you have undergone some type of extensive reno, or ducts have become contaminated, paying for cleaning is pointless. Its one thing if you have a 30 year old home that has never had a duct cleaning and you can actually see mounds of dust built up , especially in the return side, then go for it. Keep in mind that most duct cleaning companies will only get 80% of the dust , or less at best. Keep in mind that most of the dust in your home is lint from clothes and linens, and skin cells from you and your pets and is constantly being generated. Dust that builds up in ductwork , generally stays in the ductwork. The power of suggestion, scare tactics, up sell!!!
You may consider having your air ducts cleaned simply because it seems logical that air ducts will get dirty over time and should be occasionally cleaned. Provided that the cleaning is done properly, no evidence suggests that such cleaning would be detrimental. EPA does not recommend that the air ducts be cleaned routinely, but only as needed. EPA does, however, recommend that if you have a fuel burning furnace, stove or fireplace, they be inspected for proper functioning and serviced before each heating season to protect against carbon monoxide poisoning.
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