We were initially told "oh don't worry, we don't treat for mrsa" when my son contracted it years ago. It's turned into one of his more major issues now 7 years down the line. It's not a horrible thing, it's just something that flares up and often when my son is admitted it's due to the mrsa flare-ups causing issues. I'd suggest being aggressive at treating it if it's just showing up in cultures. Ask lots of questions about how do you treat it, what's the plan, what's the option if we don't treat it, etc. I wish I'd have known more before rather than just taking the CF team's words as gospel.
We are with a different CF center now. We had too many issues with things that "we don't treat" and is "not a big deal" and "oh, that's GI related". We have a CF team that works with endocrine, GI, ENT and infectious disease groups with a give-and-take and sharing of info and creating plans for whatever comes up now. Much happier.
Saying all that, sometimes the mrsa doesn't need to be treated, just ask lots of questions and judge based on how you feel more than what's in the culture. Sometimes MRSA affects people with CF with symptoms and sometimes it's symptomless.