Most medical doctors know very little about reptiles & are quick to paint them all with the same brush, ie. saying they carry salmonella. In truth, it's far more likely found in aquatic turtles, and WAY more likely your child got sick by accidentally coming into contact with a cutting board or towel that contacted raw chicken in your kitchen than anything to do with your snakes or lizards. And don't forget the grocery store! Do you use the sanitizing wipes on the carts??? People put raw meat in the carts and the packages may have leaks & germs on the outside, hint hint! Your doctor just jumped to an unfounded conclusion, IMO.
You have my very best wishes for your son's speedy recovery...while I understand your priorities, I'd not be so quick to get rid of your reptiles over this. Little kids
stick their hands everywhere, as was already suggested, plus they are smaller & have less resistance to these things compared to older kids or adults. I understand your panic...no one wants their children to be seriously ill...it's scary...but IMO it's NOT the snakes that are an issue (& I have 34 years of keeping a house FULL of snakes & some lizards, along with raising my own rodents & having multiple dogs), & as a parent of small children, getting rid of your reptiles is not any sort of guarantee that your children will never get such an illness again.