BeSha'ah tovah!
We are not familiar with an increased risk of group B strep infection associated with mikveh immersion. The water in modern mikvaot is kept to extremely high standards of hygiene. To reduce the risk even further, a woman can prepare at home (preparation rooms can present a greater risk of infection than mikveh water if they are not thoroughly cleaned) and dunk only once in the mikveh. She can also arrange in advance to be the first to immerse that night.
Although there is a widespread custom to immerse during the ninth month of pregnancy, a woman is not halachically required to do so unless she has become niddah. Uterine bleeding can make a pregnant woman niddah, but it is uncommon, especially in the last trimester.