Staffolocaucus bacteria have been around for a long time. Bacteria also live on the skin and all around us, it's just that sometimes they get tough (and we get weak, i.e. the wound) and they infect us. I wouldn't go on a mental witch hunt trying to figure out where it came from. Do watch the size of the wound -- circle it with a sharpie so you know for sure how big the red area is. Then watch to see if it's going down or increasing. If it is doing ANYTHING other than getting smaller, after a couple of days, CALL THE DOCTOR to see if your son needs a stronger medication. There are tons of antibiotics in the arsenal, and they will use progressively tougher stuff if it doesn't clear up. Your PCP should be made aware of what is going on, and be sure your doctor knows what was prescribed at the ER. Since it's a staff infection, I would think the doc's will want to monitor this closely.
(for ex.: I had a staff infection in my epesiotomy (can't spell it, sorry) after child #2. The doctor put me on some heavy duty antibiotics and had me come into the office every 2-3 days until he was 100% sure it was clearing up and healing. My now adult daughter just had knee surgery, and one of her stitch lines got infected, and they had her come into the office IMMEDIATELY, prescribed antibiotics on a Friday, and saw her again on Monday. No one cultured it for MRSA, but they did act upon it immediately. (of course, surgical wounds are deeper than scraped knees, so there's an unhealed path to the inner sanctums of the body, but even so, you need to be proactive and be sure your doctor is doing the same.)
The other thing you can do is buy Betadine. It is brown, like iodine, but doesn't sting. When you change his bandage, use a cotton swap and coat the cut and the surrounding area with it -- it is what they use to clean the body prior to surgery. And, since it is MRSA, which is a nasty little bugger, I would use a cotton swap for the infected area, and a separate, clean one, to coat the surrounding skin. And Wash your hands before and after you play with his wound.
Wash your hands thoroughly, rubbing them well under the water. The rubbing and the water flow will really help to get germs off if you scrub up, whether you use an antibacterial soap. Everyone in the family should be making a point to wash their hands before the eat, and stuff like that. Washing your hands is the #1 method to prevent infections from spreading.
Most importantly, don't panic. Be pro-active, pay attention, and call your doctor, because your doctor's office sees this a whole lot more often than you think. And someone should make a point to stay on top of this along with you -- I would not rely on the ER to be my family physician.
The bottom line is that 80% of the people in the world have MRSA living on the exterior of their own bodies. It just happens that this time, it got inside because of the wound. Be watchful and dilligent, and the antibiotic should do the trick. If the infection spreads, be quick to call the doctor. Most MRSA infections are handled fairly quickly by antibiotics -- the problem is that we hear about the traumatic ones.