Please double check with your physician. You should start the antibiotics now and continue through the course, including Yom Kippur. Be sure to drink a lot in the days preceding the fast (i.e., now) and to rest as much as possible during the fast, even at the expense of attending shul. Fasting is more important than going to shul.

There is no one-size-fits-all definition for when you should drink shiurim, but a "bad feeling" that does not improve with some time lying down could be one. Prepare shiurim in advance, just in case, with a nourishing liquid (like a non-salty soup broth) so that you get as much as possible from the drinking. But if you generally fast well, there is good reason to think you will do well fasting in your second trimester.

For more information, please see our site's related article.

Gemar chatimah tovah!