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My boy had soft stools and then diarrhea pretty much since I brought him home.  I was feeding him Complete Health puppy deboned chicken, oatmeal & salmon meal.  After three rounds of antibiotics my vet recommended switching to the prescription Royalcanin gastrointestinal puppy food.  It has worked well, he now has firm stools; when I tried to add a bit of the Complete Health into the Royalcanin his diarrhea came back.  It is extremely expensive, and I know many on this site don't like prescription food, so am wondering if anyone has any other thoughts?

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Go to the food group--they can help you--I would first say that you should have firm stools for at least a week and then add the old food a TINY bit at a time--but since that made him sick, it could be the chicken--you might want to try one of the limited ingredient foods with lamb or venison--but again, the food group can help.

Also, the antibiotics could have wreaked havoc with his balance of bacteria in the colon--did the vet offer any probiotics?

And was he tested for parasites?

Ginny's advice is spot on, and her questions are my questions: Was he tested for parasites? What were the results? 

The treatment of choice for giardia is Panacur. But many vets unfortunately prescribe metronidazole (Flagyl). 

Three courses of metronidazole without a good probiotic wreaks havoc on the gut flora, especially in young puppies. He desperately needs a good probiotic, and a limited ingredient diet. There is nothing therapeutic or medicinal in the Royal Canin Rx food; it's simply a bland diet, filled with corn, by-products, and some of the worst ingredients imaginable. You can feed a much better bland diet much less expensively.

 We can help you with choosing a food in The Food Group, assuming he's negative for parasites. But first, you need to get him on a good probiotic for a week or two. I recommend Proviable DC. Do not get Fortiflora from the vet. 

I will be sure to add my discussion to the food group. However, to add more detail, Leo was originally prescribed an antibiotic and probiotic after discovering a strain of c. diff. While on the medication, he was eating a chicken and rice diet and his diarrhea went away. At that time, we switched him back to his Wellness puppy food and his GI issues returned. As a result, he was prescribed another round of an antibiotic/probiotic concoction with the chicken and rice diet and, yet again the diarrhea was gone. For the last time we put him back on the Wellness food and eventually switched to the Royal Canin when his Gi issues remained.

What was the probiotic? Did you give it at least 2 hours apart from the antibiotic? That's important; otherwise, the probiotics are basically cancelled out. 

They usually do need to be on the probiotics for a couple of weeks after the meds are discontinued, especially with metronidazole, in order to establish a strong colony of good bacteria in the gut.

And it does sound like he needs a limited ingredient diet.  

My guy had Gardia and i had no idea..... 

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