Hi Donjoe,
I was infected with at least RMSF at the age of 5. At the age of 44 I received my first round of abx for not only Lyme, but all co-infections. My LLMD had to clinically diagnose me.
I was on oral abx treatment for a full year before I was capable of testing positive.
Have you tried presenting your doc with some of the scientific studies supporting the fact of congenital LD? They are easy enough to find by using Google Scholar.
I wish you the best of luck with your son - I'm certain both of my now adult children have been infected either since birth, or were infected shortly thereafter.
There is a skin condition that LD can cause - I think this is something I am dealing with as well- which can be found here:
emedicine.medscape.com/article/1051695-overviewHopefully you will find what it is that is affecting your son soon!! I hope we were able to help some!!