The main risk with group B strep is passing it on to the baby which is why they give you antibiotics during labour. Generally if you've had antibiotics on board for long enough before bubs is born ie you don't have a 2 hour labour or something like that the baby will be well protected. If there is any concern about your antibiotic cover the paediatricians will usually screen +/- treat the baby to ensure the baby is ok. GBS infection in newborns can be very nasty so I would take your docs advice.