Nystatin Before or After Brush?

My wife just had corrective oral surgery for both her upper and lower jaws.   After the surgery she was prescribed the following to keep her mouth clean:
1) Salt Walter Solution
2) Teeth Brushing
3) Chlorhexidine-Gluconate 0.12% (oral rinse)
About a week after the surgery she was diagnosed with Thrush and was given a Nystatin oral suspension.

Can you tell me:
1) How she got thrush in the first place (I thought we were brushing her teeth good).
2) Wheither she should use the Nystatin before or after her brushing/oral rinsing.

[Jerome Tsang, DDS]

1) The chlorhexidine and antibiotics she was probably prescribed is great at killing bacteria, so much so that the bacteria population was reduced significantly enough that the fungus had no competition.  The fungus then began to overgrow into the area, resulting in thrush
2) I would recommend the Nystatin after the oral rinse.  I believe thats the bigger issue at the moment.