Thrush is caused by Yeast, which is a fungus, not a bacteria. They will treat the uti first because when given antibiotics, the good bacteria as well as the bad are killed off. This allows for yeast to take over the vaginal canal because the good bacteria aren't around to keep it in balance. So treating the yeast and the uti at the same time wouldn't be as effective because you wouldn't have your body's good bacteria to help the antifungal kill off the yeast. They will give you antibiotics for the uti and then most likely treat you with antifungal for the yeast infection. If you need relief from the burning and itching of the yeast, ask your doc if you can use monistat cream while they treat the uti. There may be drug interactions that I'm unaware of, so make sure you ask first :)
Actually yeast is not good when baby is going to pass through the birth canal... but you are still early. If they are putting you on antibiotics take probiotics with them & eat plain greek yogurt. Every time I have ever had to take antibiotics I eat tons of greek yogurt & take probiotics & it keeps me from getting yeast infections.
I also squirt greek yogurt up inside & yeast goes away... but that's just me, don't do that until you have personally done your own research.
Are you talking about thrush? If its thrush in the vagina that is just basically a yeast infection... caused by a certain type of bacteria. (I think). I don't think it affects the baby. Good luck and I hope you get it taken care of quickly!