Evidence now shows that perhaps your cat is not entirely to blame. At the 100th General Meeting of the American Society for Microbiology in May of 2000, a study was presented that pointed to microbiological degradation as the cause for stinky carpet.
Jodi Martin and J. Joyce, researchers at Calgon Performance Chemical Group in Pittsburgh, PA felt that the odor of cat urine in new carpeting was a significant enough occurrence to merit a study of the cause. They hypothesized that the odor could be caused by a) microbiological degradation of the carpet backing or b) chemicals used in the manufacturing of the backing. Subsequent lab findings pointed to microbiological degradation as the probable source.
What Does This Mean? In lay terms, tiny microorganisms (bacteria) find a home in the latex backing of the carpet, and during their growth produce butyric acid, which is a weak acid that will not harm the carpet, but does have a decided odor that to some humans (and cats apparently) smells like cat urine. This particular bacteria appears to be anaerobic, which means it is capable of growth outside of oxygen. The standard disinfectant used in carpet manufacturing apparently does not affect these microorganisms, and any new disinfectants will need to be tested to ensure they do not harm the latex backing.
I have written Ms. Martin, asking if any new breakthroughs are on the horizon, but have yet to receive a reply. It is thought though, that the issue is serious enough to carpet manufacturers that Calgon will want to follow-through on it. In the meantime, unless you catch your cat "red-pawed" urinating on your brand new carpet, consider that he may not to be at blame for its odor. If you have any doubts, you can try a black light, which will cause cat urine to glow. Once identified, you can use the proper cleaning steps to remove it.
Thanks to my forum members BalletCatter, for nailing carpet odors as a problem source, and GalensGranny for diligently hunting down the facts. Their efforts were, in large part, directly responsible for this article.