The vet said there's no way to know how it got in the house or in her pen, but he said there's nothing we did or didn't do that would cause it.
When I googled it, it said the way to avoid it is regularly cleaning the pen and avoiding overcrowding. My wife cleans up the pen two or three times daily, including changing the pads in the litter boxes, and changes out the fleece bedding and washes everything down with vinegar water every week. Daisy and Rose share two Midwest pens, so they have a bit less than 16 square feet, so overcrowding isn't really an issue.
Daisy is completely fine. I'm not sure why Rose was affected and Daisy wasn't, but I'm glad it isn't worse.