Vet got the result of Zion's first stool sample.  He's 11 weeks old now.

The only symptom of Isospora is diarrhea and his stool has been fine since we got him.  Is the treatment necessary?

He is healthy in all aspects (behavior, appetite, solid stool, etc).

Does the bacteria disappear on own later?  Would he get worse?

I just want to ask here as an external opinion on top of asking vet tomorrow.  I just don't trust vets in 'optional' things as I feel like they're just out to make money.

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boy, that's a great question, and I will be interested to hear what others think. Bertie also had a bad poop sample when I brought him home at 9 weeks, and I went ahead and treated him, as I figured he was young, stressed in his new environment, and didn't have a fully mature immune system yet (also, we lived in NYC, and I felt he could easily be exposed to god-know's-what, so was feeling paranoid at the time). I think most vets do treat (not just to make money, but also to cover themselves in the event you don't treat and then something happens, and also because that's what they've been taught to do), but it is an open question. It's very very common and most dogs are able to deal with it on their own (with maybe a little kaopectate or something if they do get a tummy upset). So I would say the choice is yours to make.
I had the exact same thing happen with my cardi puppy. His poops were fine, no diarrhea, and the vet said he was perfectly fine at his vaccination appointment. But when they got his fecal back they said it was positive for coccidia and to treat him.

It is my understanding that some dogs are just carriers and will not show any symptoms of coccidia. As a dog ages they build up an immunity which is why it mostly affects young puppies. Since it can be transfered so easily I did treat him for it, as I wouldn't want anyone else's puppy to get sick due to my dog, but since it's so ridiculously hard to kill I'm not sure that he won't be re-infected anyway. Regular household cleaners don't kill it, and neither does freezing. I think you have to use bleach, ammonia, or boiling water, and spraying my entire yard with that is just not very realistic.
My older pup (Jon) was diagnosed with coccidiosis at his first well-puppy visit (13 weeks old) and since he was presenting with mild diarrhea and no interest in food, we had him treated with the drug Albon. Coccidia is a parasite that tends to only show itself (symptoms) when a dog is stressed (such as a pup moving to its forever home). Some dogs can carry the bacteria their entire lives with no symptoms. If Zion has symptoms, albeit mild, please consider the treatment (not sure anything other than medication would be warranted). Did your vet recommend a treatment other than preventative medication? Was the cost of the drug outrageous? If so, you might want to seek another vet's opionion.
I just wanted to throw out there that I had to treat both my dogs, at different points, with Albon and it cost me $4.50 for a full course of treatment, so if the vet is recommending it, the reason in this case would most certainly NOT be to make money.

Jack tested positive as a puppy. I looked into it, found it is very common and tends to "bloom" when dogs undergo stressful transistions, many adults are asymptomatic carriers, and it can in some cases cause severe bloody diarrhea. I figured why risk waiting and treated.

We just had our dogs for their annual fecal and my nearly-six-year-old female came up positive. I had dropped off TDI paperwork, which requires a negative fecal, and the vet can't sign off on the paperwork with her positive fecal. She has no symptoms. The vet did say that usually adults don't get symptoms, and moreover they will shed in one sample and not shed in the next sometimes, but in the end he recommended treating. Again, the Albon was $4.50. So we ran the treatment course mostly to get a negative fecal for our paperwork.

Puppies can go downhill very quickly with diarrhea, and at 11 weeks they are still also susceptible to Parvo if they are in a weakened condition, so if it were me I would definitely go ahead and treat rather than risk having the Coccidia levels rise as they reproduce and have him become symptomatic suddenly.
P.S. I hope I don't sound harsh, but if you genuinely believe that your vet recommends treatment, or not, based on making money then I strongly encourage you to find a vet you trust. Vets are NOT salesmen working on commission. They are highly educated professionals who went to school for many years, and go to ongoing education seminars throughout their career, to learn treatment options for your animals.
To answer your question, most pups do get coccidia, especially from the stress of ownership change. Uncontrollable explosive diarrhea is not fun, it dehydrates him and its a pain for you to clean up. Treatment is relatively cheap, $12 for 2 wks of Albon. Vets don't make that much money in the first place and they certainly don't get rich by writing you cheap Rx.

Bottom line: It really depends on Zion's immune system.
Thanks for all the help guys! His third round of shots are coming up in 2 weeks, I will get him treated at the same time to sweep them all.
Treatment is cheap, don't risk it
My vet prescribed Ponazuril, it came in refrigerated syringes and was given orally (which my pup had no problem eating). Once a day for two days, and that was it. Very easy treatment.
YES TREAT HIM! If you don't treat him he will continue to shed the parasite and infect others. Treatment is easy and cheap.

Also, reinfection isn't really as common as everyone keeps saying. Usually if you treat the pup once and get rid of the initial infection it won't get reinfected. Pups usually get it from their mom, who is shedding the parasite, and at that time their immune system is not developed enough to fight the infection. By the time you get the puppy and treat it its immune system is much more developed and reinfection is unlikely. With Franklin I only had to treat him once and he had a negative fecal after that.

And I really have to defend vets here. They are not just out to make money. If you truly believe that then you have a bad vet. They have dedicated their lives to the health of our best friends and if they were in it for the money they would be human doctors, its much easier.

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