Basically, he's got staphylococcus epidermidis, or "staph epi", as the doctor called it. It can be a concern because it can cause issues with The Boy's port. They're going to keep one of the antibiotics going until his blood counts recover. The other one will keep going for 7 days after the negative result. They aren't particularly worried about it, but they want to proceed cautiously.
And, the doctor left the door to the room open when she left. What, do these people live in a barn? Hello: IMMUNE COMPROMISED CHILD. Close the frakking door!