STBYRUD, it is my belief that there is no prohibition on flying with antibiotics per se. However, some guidance on this and other medication and ailments is to be found in
AIC 99/2004, the current issue of "Medication, Alcohol and Flying".
The relevant paragraph is 2(a), which states:
(a) Antibiotics may have short term or delayed side-effects which can affect pilot performance. More significantly, however, their use usually indicates that a significant infection is present and thus the effects of this infection will almost always mean that a pilot is not fit to fly.
You might read para 6(c) too :
(c) Have I given this particular medication a personal trial on the ground of at least 24 hours before flight to ensure that it will not have any adverse effects on my ability to fly?
Hope this helps.