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Even if you clean a pet stain with soap and water certain micro-organisms remain behind and your pet can smell them. Enzymatic Cleaners are designed to completely eliminate the source of the odor by using enzymes to eat away the micro-organisms that cause the odor. The one draw back to these cleaners is that they are slow; it could take several weeks for them to completely elimiate an odor.
Enzymantic Cleaners are available at most pet stores, organic/natural/health food stores, and even some hardware stores. You can also ask your vet for suppliers.