Your dictionary is right, Lara, it's just that "organism" isn't usually applied to humans. Normally you only see that word in science context, when talking about, I don't know, bacteria or something like that.
Your next suggestion of "system" is better, but it still sounds kind of funny. That's also a word that people don't normally use when speaking of themselves.
The word most people would use in a sentence like the one in the story would be simply "body":
"It's preventing germs from entering my body as we speak."
And I think you have a great vocabulary. Your English is a million times better than my non-existent French!
