Anything that lowers your immunity is going to allow the Lyme disease to run rampant. There is a small group of lyme disease patients that develop Crohns as a result of the borellia infection. Lyme disease lowers your immune response which can allow other pathogens to get a foot hold in your body.
My wife has Lyme disease and I am the one who has treated that and the two coinfections that came along with it. I also treat my own Crohn's disease.
It is pretty likely you have also picked up a coinfection with the Lyme. I would get tested for Bartonella and Babesia and those are just the more common coinfections. There are others.
A Lyme literate Doctor is also a good idea (LLMD)
A short course of antibiotics will not resolve the disease unless you have been infected in the last couple of weeks. That is the typical treatment and it is inadequate.
Good luck.
Dan