We are looking into using metabolic cages for urine collection, and wanted to know if there is a protocol that is commonly used, in order to help prevent contamination from fecal matter, and obtain a pure urine sample.
To obtain urine absolutely free of any fecal contamination to serve as a blank sample for determining any forbidden added exogenous steroids in the urine, we inserted a catheter into the bladder of calves. Thus we prevented any run off from the skin or other tissue which might be containing foreign unwanted substances.
Midstream urine (considered to be less contaminated or sterile) might also a possibility but it still comes into contact with tissue on the outside of the animal.
See the attached paper. It might prove to be a solution of your query. Also find a link to a previous thread in RG where this matter was discussed before.