Hey Jen,
A few follow-up thoughts: First, CFers colonize bacteria even when they are doing treatments from day 1, so that your center didn't have you start until recently doesn't meant that is why your little one cultured MRSA and pseudo. Second, I think most here are proactive in their approach to CF, but there are some doctors who aren't. So you do need to have the discussion with your doctor (we aren't trying to give medical advise but our thoughts based on our experience). For me, proactive is 2x a day Alburterol/Xopenex and 2x a day percussion (and later vest) and by 6 months Pulmozyme and by 2 hyper-sale. And when sick more. It may be your doctor is open to a more proactive approach if you discuss. Or that you decide you want a different doctor who is more proactive. But you'll need to discuss to find out their medical expertise and maybe get a second opinion if you aren't comfortable with it. And it will likely also be based on how they want to handle MRSA and pseudo. Again, personally, I'd want to try for eradication and believe at least with pseudo that that is concerned "standard of care," (I think MRSA isn't clear yet which is that article I posted).
Finally, one other "red flag" for me was that you could see your results without talking to the doctor. Most health systems will only release the results once they have been reviewed by a doctor, but it doesn't sound like anyone called you on them, and I would think they would have when they reviewed for them to be released, so I wonder why they didn't call you? Just another thing to maybe ask when you talk, "I'm wondering if I need to call or if the doctor always calls me when there is a new bacteria cultured."
Hang in there mom. Praying for you all.