They tested for a yeast infection, chlamydia and a bacterial infection all came back negative, but they said I could still have a bacterial infection they didn't test for. It has cleared up a lot, no more green discharge, not much discharge at all and the itching is almost gone. So I'm kind of torn. Also, does anyone know if a bacterial infection affect ovulation?
Honestly, because they react with your current medication, I don't blame you for being hesitant.
IF I remember right (intro microbiology was a few years ago). Bacterial come in gram negative and then gram positive. So antibacterial drugs can be made to go for one or the other by specifically targeting that difference (there are also other differences they can target out). Some drugs however work against all kinds of bacteria. Some of the common bacterial infections are chlamydia, syphilis, gonorrhea, and then I think staphylococcal. However, it's still possible to get other infections besides them.
Your doctor probably ruled out yeast infection because of the green discharge/ how it looked, which leaves bacterial infections. Now because there are tons of different bacteria they can only test for so many. So it quite likely that yeah your infection is bacterial and will need an antibiotic to treat it.
However, if you're really concerned about a reaction to antibiotics from your meds you should call up your pharmacist/ dr office (especially if the reaction can be dangerous).