I think I'd rather over cautious than under cautious when it comes to health. Vaccination does not mean you are immune to getting the disease, it promotes antibodies which can help to prevent the disease or fight it in the event you are exposed.
Well, it's going around, a lot of vax'd kids get it and those are the early symptoms, so it makes sense to swab for it. Definitely better safe than sorry. Plus the antibiotics only work if they start them in the early stage of the illness (before the 'cough').
My 6 week old has tested postivie for WC. I think your doctor is fantastic for testing so early. It is a horrible disease and anyone can get it regardless if they are vaccinated or not. Vaccination only has 80% coverage. Hope all is well.
Bookmarks