Feeling horrible after starting antibiotics for a long term Lyme infection is really common. I always check out the side effects lists on a new medication so I can pay attention to what's happening to me.
Sometimes, it's hard to differentiate side effects from herxing/die off, such as fatigue or stomach upset. But in my own experience, when an antibiotic made me feel like death warmed over, or turned me into an anxious, trembling, unfocused mess, those were herxes.