Unfortunate situation. A good vet might be able to help.
Most cases of babesiosis resolve without any specific treatment. For ill patients, treatment is usually a two-drug regimen. The regimen of quinine and clindamycin has been used, but is often poorly tolerated; recent evidence suggests that a regimen of atovaquone and azithromycin can be equally effective . In life-threatening cases, exchange transfusion is performed. In this procedure, the infected red blood cells are removed and replaced with fresh ones.
Veterinary treatment of Babesiosis does not normally use antibiotics. In animals diminazen (Berenil), imidocarb or trypan blue would be the drugs of choice for treatment of Babesia canis rossi (Dogs in Africa), Babesia bovis, and Babesia bigemina (cattle in Southern Africa).
There is a vaccine that is effective against Babesia canis canis (dogs in the mediterranean region) but this is ineffective against Babesia canis rossi. Babesia imitans causes a mild form of the disease that frequently resolves without treatment (dogs in South East Asia)."
Some other web pages on the condition:
http://www.marvistavet.com/htm l/body_babesia_infection_in_do gs.html