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Pneumonia Vaccine? Yes or no??

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DS 13 has been stable for 1 year.  He has been  out of school for 3 years so as a result little to no colds/infections/viruses for a good 14 months.

He was treated for Bart/Pans with anti b's and herbal protocols.He is finished and healing. He has not had so much as a cold in 2 years since we pulled him from school.  But he still has some immune compromised lab results. His immunologists wants him to do the vaccine test in case he needs IVIG for insurance purposes and also bc he has little to NO immune protection for pneumonia.     I am afraid this vaccine  will ROCK the boat.  BUT doc feels that when he gets back to school again infections will follow so vaccinate over this summer is needed.  So afraid it will start things up again.  His IgA and IgG are on the low end but not horrible.

On a side note he eats completely clean and strengthening his immune system thru clean eating and supplements was our plan. 

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