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Friend, it sounds like Cooper has a pinched nerve along the back as a result of a bulging disc. The disc is causing compression on the nerve (spinal cord) interfering with the motor function of the back legs and causing the fecal and urinary incontinence. Less likely we can also see similar symptoms with arthritis of the hips.
I would recommend a hands on examination by family veterinarian and xrays of the spine and hips as initial screening test. In addition your family veterinarian will start him on prescription anti inflammatory medication. In the meantime you can begin to supplement with Cosequin (glucosamine) given at label dose. You can buy cosequin over the counter in any pet store.
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It is possible he could of had it. But, if he wasn't showing any symptoms at the time that he went to the shelter then they don't need to test for it. Plus, many times in the early stages plain xrays will not show any lesion. He would of needed advance imaging like an MRI or Myelogram which is only done in patients that are showing symptoms.
Please reply if you have additional questions.