"A number of autoimmune diseases are thought to be triggered by infections," says Eisenlohr. "The results of this study suggest that certain antibiotics used to treat those infections may also contribute to that trigger."It's complicated, but basically their idea is the antibiotics cause altered proteins that the body identifies as 'foreign" and then attacks them.
I have always assumed that the antibiotics kill off most, but not all of the infection, leaving a residual population of resistant bacteria that although not clinically detected, triggers the autoimmune reaction.
Either way, the solution seems to be part of the problem.