The thing is, it's an anaerobic bacteria - meaning it can only thrive in low-oxygen environments. That's why it's so important to clean everything thoroughly with water and never let anything stagnate. I'm not sure where it could have come from, but if you don't find the source it may come back. :/
I don't wish that kind of thing on anyone, let alone a cute little duckie. Oh, the poor thing...I hope she continues to improve. You're one quick-thinking duck mama!