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Cancer or bacterial infection mitigated by immunosuppresant

On week later, he wasn't feeling well so I lowered the Atopica to 100mg a day but kept using the ketoconazole. He improved but still looked sick.  yesterday he was noticeably lethargic and had alot of trouble with mucous coming out his nose and licking his paw.  Iit was swollen all the way to the elbow.  His toe where the nail was cut short was the one he was licking and it was discolored but the nail looked fine now.  I took him to the vet.  I was not looking for blame, but the doctor kept leaning towards cancer and said it was "highly unlikely" the infection was from the nail trimming three weeks before and the anemia rarely is caused by an infection. He prescribed baytril and another cbc in 4 days to see if the HCT is still low.  No other instructions.  Seemed heavily opposed that the infection was the cause of the anemia.  Said it was just a coincidence.  Atopica states in the product label included with the pills, "Atopica is a potent systemic immunosuppressant that may increase the susceptibility to infection and the development of neoplasia."  I am stopping his Atopica all together because as far as I can tell, it seems like it is suppressing his immune system and not allowing him to fight this infection for the past three weeks.  Can a bacterial infection in the blood cause anemia and this not be cancer?  If it is just an infection will the  Baytril help him and will the cbc show that in just 4 days?  
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Actually atopica is a treatment for anemia (if auto immune hemolytic anemia), so Atopica is not necessarily to blame.  Atopica/ketoconozole is appropriate excellend therapy for perianal fistulas as well.  I would talk with your veterinarian when adjusting meds, as he/she may agree it's fine to stop for the time being, but needs to know what other meds are being adjusted and how your shepherd is doing with these adjustments to help determine the best therapy options for your pet.  Repeating bloodwork is certainly beneficial, but a chemistry baseline bloodwork would also be beneficial (additional bloodwork).
"Can a bacterial infection in the blood cause anemia and this not be cancer?"
Bacterial infections such as the bacteria that cause lyme's disease and ehrlichia can cause anemia.  Cancers can cause anemia as well.  More diagnostics are warranted to get answers.
"If it is just an infection will the  Baytril help him and will the cbc show that in just 4 days?"  You may see a result in 4 days or it may take longer.  Either way - a cbc is just a snap shot during a race -- what's happening in the 4th lap cannot be predicted by the first lap status.  Certainly check in 4 days, as if the rbc's drop and anemia worsens, other therapies, possibly a blood transfusion, will need to be started -- so keep up with those CBC's.  Hopefully the baytril will be all that's needed.

Again, please talk with your veterinarian.  He/she may have been inclined to start a steroid (used for autoimmune hemolytic anemia and as a cancer drug, but not a good choice first line cancer drug), but elected not to do so for anemia as it was likely known atopica was on board.

I hope for the best for your Shepherd.
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