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Bitter apple wont' help here, since it's only good for animals who chew things.
Since this behavior started after she had the infection, I really think this is related. There is always a reason when cats start avoiding the box.
She may have had pain when she went in the litterbox, and then got more pain when she was straining to go. This made her think the litterbox itself is causing the pain, so she tried to find a place where she could go without pain.
If you're sure she's healthy and not painful , you need to confine her to a smaller area, like a large dog crate, with a litterbox and little else until she is using it reliably. You must do this no matter how long it takes. The shelter will surely kill her, since they cannot adopt out a cat who is messing on the floor.
I agree that going two or 3 times a day is a lot. What and how much are you feeding her?
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