You might want to ask your vet about a urinalysis as well as a culture and sensitivity. Not all antibiotics work for all infections. My dog developed crystals in his urine after being on the wrong antibiotic. Only a culture and sensitivity can confirm the type of bacteria present. Our dog ended up with a bladder stone as a result. Recently my other dog was diagnosed with a UTI and the bacteria she had required four weeks of antibiotics to make sure it was gone.
As an aside dark smelly urine sounds more like something with the kidney and i would be doing a full chemistry panel of bloodwork of it was my dog.
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