You are doing a great job. Sometimes kids just get sick- a lot. I think talking to a naturopath is a great idea. You don't mention how old your son is, but I think it's great that you are still nursing him. You really are doing more than most! The only things I would suggest is looking at your household cleaners- are you using safe, natural ones, or lots of bleach, etc? That can make a huge difference. I know of a family whose child had asthma, though no one in their families had it, and they found out it was a reaction to their toxic cleaners. They changed them, and he was no longer hospitalized for asthma.
I would also suggest seeing a pediatric chiropractor. They can do a TON to help kids whose systems are overloaded, or having a hard time. This website can help- http://icpa4kids.com/index.php. I had my son see a chiropractor from 1month- 1 year. It was very helpful.
Don't be afraid to let him get dirty, play outside, and play with other kids. I think most kids go through a period of getting sick a bit and building up their immune system. Every time my son gets a virus, I remind myself that he won't get it again, because he's built up his natural immunities. The worst thing parents can do is keep their homes pristine and "free" from germs. Kids' bodies need germs around to know what to fight off, otherwise, they get a lot of autoimmune problems because their bodies aren't sure what to fight. Do some reading- you'll find that kids that grow up on farms have the strongest immune systems, BECAUSE of what they are exposed to on a daily basis. So take him to a petting zoo, get him out and about, and try to relax a bit and know that you are doing a lot to help him. :)
Sorry to be so long-winded here. Two other suggestions to try- probiotics, and fish oil every day. Cannot hurt, but can help! :)
Good luck to all of you!
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