Serious. These are the worst places to have infections. Your doctors will be vigilant and aggressive in treating infection in the brain tissue and spinal cord. These infections can be in the covering of the brain/spinal cord or in the tissue itself. Each requires different treatment. They usually come from another location and spread to the central nervous system. I hope your son does very well.
Need more data. You have mentioned problems that could be very serious or not based on the suspected or confirmed germ. Once you provide us with the data we can be more specific with our information.