Thanks for the query to H.C.M. Forum .
The main fear is that you have infection and causative organism may be one , so blood culture
and sensitivity test will reveals many things.
As we will be able to find out which drugs will suit you most for bacterial infection.
This thing , you have not mentioned in your query.
Behind knee may be a cellulitis
due to chronic bacterial infection.
For Hashimoto's , you are already taking treatment.
In my opinion doxycycline is a bacteriostatic drug and will not effect much.
So consult your treating doctor & get his opinion regarding this.
Get well soon.