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Hello JC, Nystatin is not absorbed orally so as soon as diarrhea stops, start with treatment in pediatric dose. Please give extra sugar water or pedialyte liberally meanwhile to obviate dehydration. There should be no concern about other side effects as it is not absorbed.
At the most you could give her probiotic powder or drops for the duration of treatment with nystatin.
Formula feeds can be continued as per schedule and any type of fluid can be given in between according to her acceptance.