Not sure I understand, as you already have strep and are already taking antibiotics for it so even if this were a risk, and it's not, you'd only be exposing yourself to yourself. Also, whoever told you urine kills bacteria is someone not to listen to anymore. While there are some things in urine that might be antibacterial, there are more things in it that are. It's a waste product the body intentionally discarded. Listen to your body. Peace.
It's doubtful anything will happen from that. I'd not worry about it unless you get some type of symptom which you really likely aren't going to get. Women have step b in the vagina frequently without harm and it is only an issue if they are about to give birth because of the baby. This is where you hear about step on genitals more. Urine is not really sterile and can contain bacteria of its own. Peeing in a bottle is different than oral sex by the way. I really would not worry about this and not expect you to develop symptoms.
EDIT: I went to the bathroom and peed on the toilet IN MY HAND and poured that on my penis not the one from the bottle.