pseudomonas can be found almost everywhere (skin, mouth, throat, etc) so it is possible that it was just in his throat and not in his lungs. The throat cultures done on toddlers are not as accurate as the cultures done on actual sputum that is coughed up. If you are really concerned about this, I wouldn't hesitate to ask your CF DR or CF Nurse (I email my daughter's CF nurse with questions quite often).
I am suprised your DR didn't put Ethan on Tobi and Cipro (that is what the recent studies are showing to be the most effective for eradicating pseduo during the first cultures with it) so you might want to keep that in mind for the future if he cultures it again. TOBI is questionable in children under 5 bc there aren't studies that have been done to keep track of side effects on toddlers-meaning it could possibly do more damage than just hearing loss (like that isn't bad enough!) and it made me VERY nervous to have my toddler take it...but she got rid of the pseudo (had a CT Scan done to make sure it wasn't hiding in there) and hasn't cultured pseudo for her last 4 cultures (knock on wood!). I worry each time that she has a culture done that pseudo will rear its ugly head but (as much as I hate for her to be on these meds) I want to treat them aggresively if they are there to prevent any lung damage.
Pseudo can be very tricky bc it can hide in the lungs (it also develops its own biofilm that keeps it protected from antibiotics) and each culture done only tests a small amount of sputum that came from who knows where - meaning that the pseudo could be camped out in a lower lobe while the sputum tested came from an upper lobe which would lead one to believe there is no pseudo which wouldn't really be the case. Once a toddler cultures it, most docs now days are saying something like: 14 days Cipro with 28 days TOBI, then TOBI every-other month until there have been a few psuedo-free cultures done. They used to say that people couldn't get rid of pseudo, but now they are finding that if it is caught right away and treated aggresively, it can be eradicated - which is why most/hopefully all clinics are doing sputum cultures at every visit even if there are no signs of infection. However, for those who aren't able to eradicate it soon enough, once it sets up camp in their lungs, TOBI and other drugs are used mainly to control it, not really to get rid of it.
Oh ya, my daughter cultured pseudo twice almost a year ago and showed NO symptoms at that time.
Hope this helps!