I took Doxycycline which is the recommended antibiotic against Lyme disease. There is no empirical evidence that taking antibiotics for longer than two weeks helps against Lyme.
Citation needed... THERE, I finally found it http://cid.oxfordjournals.org/content/31/4/1107.long Okay, this was an extreme case. I was mistaken, the woman took the antibiotics for a longer time and intravenously. However, it's still true that the risk of fungal infection is increased by a substantial amount.
Here is another case displaying the dangerous effects of long-term administration of antibiotics which resulted in death http://cid.oxfordjournals.org/content/51/3/369.full (but not because of fungi)
This way of treating Lyme Disease literally kills people, I am not exaggerating.
There is no magical barrier. Some young children have been infected with extremely virulent Lyme after only 15 minutes of nymph tick attachment. More (experimental, not rhetorical) research is definitely necessary.
The comment about fungal infection destroying one's body badly needs a citation.