Response to treatment can define the likely cause. If the problem doesn't respond, sometimes more diagnostics are required. Certainly fecal exams are an early diagnostic, and more advanced fecal diagnostics come into play in searching for the cause. The basic early treatments for uncomplicated diarrhea include witholding all food for a day, and then giving bland food in small increments. Fluid maintainence in dehydrated animals is essential.
Additional therapies address the suspected underlying cause.
The two questioners here are asking about a lack of sustained response to treatment. When one has dismissed common intestinal worms as a cause, and other serious illnesses don't seem to be a problem, metronidazole is a good therapy to try. This drug is active against many types of bacteria, especially anaerobes that some suspect play a role in an unbalanced gut flora. I can't comment on the stool being negative for bacteria. Stool is loaded with bacteria, in fact bacteria comprise a major part of the bulk of most feces.