Emily is a little older, but we only treat her staph when she is symptomatic (i.e. a 2 week course of Bactrim when she develops a secondary infection when sick w/ a virus), due to concerns about it becoming drug-resistant and/or increasing the chance of her colonizing PA sooner. We feel that acquiring PA earlier would do more damage than the usually-asymptomatic staph she colonizes.
None of us want to sit back and risk our children experiencing lung damage... it can be a hard call to make and their drs are likely to feel strongly about it one way or the other (studies have shown benefits to both approaches- treated kids do have less staph, but lung function tests, etc between treated and untreated kids are generally about the same). But all our kids treatment is so individualized and what works for one might be wrong for someone else. This is how we approach her care, though, and what I am comfortable with.
<a target=_blank class=ftalternatingbarlinklarge href="http://www.news-medical.net/news/2007/11/16/32563.aspx">New clinical standards on the treatment of patients with cystic fibrosis</a>