Hi Claire,
I am not a doctor, but maybe the reason there is no bacteria from the vaginal swab is because the antibiotics are working? I have to take some antibiotics too for an ingrown toenail. I hesitated for weeks, until my foot was that sore from limping, and my toe was just gross (sorry, TMI). I figured the infection would be worst for bubs than the antibiotics, which my doctor and the chemist both assured me were safe.

I suggest to trust your doc, or seek a second opinion if you are unsure. Some things are safer for bub than the alternative infection, but if you feel uncomfortable, def get a second opinion before stopping them. after all, antibiotics work better when you take them consistently, so better not to take them haphazardly then create a stronger bacteria!

All the best