Keep in mind that diarrhea is not a disease but a symptom of a disease and can result from a large number of possible causes such as bacteria, viruses, parasites, poisons, allergies, foreign bodies such as bones, and many more. The point that must be made is that because a pet’s diarrhea can be the result of so many different initiating causes, a detailed history of the problem coupled with a systematic diagnostic approach is the only way to discover the true cause and, consequently, the proper therapy to use.
Some causes of diarrhea which are frequently overlooked or difficult to detect are food allergies, chronic whipworms infestations, yeast infections, one celled protozoan parasites such as Giardia, resistant bacterial infections and inflammatory bowel disease.
Food allergies can often be ruled in or out as the cause of diarrhea by putting the patient on a very restricted non- allergenic diet, such as lamb and rice. Intestinal parasites, known as whipworms, are frequently present in such small numbers that they can easily be missed by routine laboratory methods. Worming for whipworms even though the fecal test turns out negative is sometimes the only way to detect the presence of these hidden whipworms and stop the diarrhea.
Giardia is a one celled intestinal parasite that is so small that, even with the microscope, it is very hard to see without the use of special diagnostic stains. Inflammatory bowel disease (IBD) usually causes repeated bouts of diarrhea. An endoscopic exam where biopsy samples of the intestinal lining are surgically removed and sent to the laboratory for a histopathology report, is the only way to absolutely diagnose IBD. Certain types of bacteria like E. coli and Pseudomonas are resistant to many antibiotics and, therefore, an antibiotic sensitivity test must be performed on a stool culture in order to find an effective antibiotic which will put an end to the diarrhea.
From the above discussion, I think you can easily understand that diagnosing the cause of chronic diarrhea is no easy matter and takes time and money to sift through all the diagnostic possibilities.