Hi, Bill. Let me tell you first of all that I am very sorry for what has happened to your child. It's tough, and you are in our prayers.
Infections do funny things to the human body for several reasons. First, the viruses, bacteria, and other organisms that cause infections damage organs, like the brain, through the poisons (toxins) they produce as they grow and reproduce inside the body.Second, when the body's immune system reacts to the infection and the poisons, the white blood cells also produce chemicals that affect organs. This is why doctors sometimes give medications to tone down the immune response to the infections at the same time that they give antibiotics or other medications against the infections themselves. Finally, some medications against infections may cause allergic reactions or other kinds of damage on their own.
So you see, Bill, the infection your son got may have triggered a combination of these events and resulted in his current situation. Fortunately, we live in a time when medicine and science are jumping by leaps and bounds, and you can always get second, third, and fourth opinions on your child's case. Who knows? You might stumble onto the right treatment, or the treatment may find him too.
In either case, keep up your spirits and your never lose hope. Best of luck.