Hi Katie,
I think this is a great question. My doctor wants me to stay in on windy days or if I have to go out I have to wear a particulate mask. Wind can spread all kinds of things. I would assume bacterias as you mentioned -- but also molds, pollen, and particulates from all kinds of air pollution which has been even worse from global warming. In fact, we are even getting pollution from places like China blowing our way.
Best case scenario is to stay indoors. If you have to take the baby out -- I've never seen a particulate mask for a baby, but the next best thing is a silk mask (again maybe no baby masks) because the fibers are very close together, or you can just using a silk scarf to cover the nose and mouth. Of course I would check with the doctor to make sure this is appropriate for a baby.
From my personal experience, I have gotten horrible exacerbations that were triggered from being outside on a windy day without using a mask.