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While I agree with you that antibiotics are very over-prescribed and it has created resistant bacteria, I think that I do need to point out that pneumonia can be either viral or bacterial. Antibiotics only work on bacterial infections. I think that the majority of the pneumonia cases associated with H1N1 are viral, rendering antibiotics useless in treating it. Take antibacterial soaps/alchohol based hand sanitizers. Alchohol actually encourages cold viruses to grow, it doesn't kill it. Where as good old soap and water while vigorously rubbing your hands will do the trick for both.
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As silkiechicken already explained, vaccines work by exposing you to a low dose of the virus (either live or dead). This triggers your body to produce its own natural antibodies to it without enough exposure to the virus to make you as ill as you would be with full exposure to the live virus.
You also mentioned chronic fatigue as being associated with vaccines, ironically the new research finds that there is a virus associated with it. This was on a recent science Friday, I'll hunt around for a link. Of course it's still in the beginning phases of this course of research, but it's still a pretty interesting finding.