You wrote "'Vaccines also cause the diseases to mutate, so if you vaccinate against pertussis, it encourages another form, parapertussis to develop."
I answered "Pertussis does not mutate into parapertussis." Nothing in your CDC quote says otherwise. I'll explain why.
The vaccine knocks down Bordetella pertussis (which is toxic) to the point where B. parapertussis (which does not carry the pertussis toxin) becomes dominant.
As a bacterial vaccine takes on the most common bacteria, the less common serotypes eventually become dominant. B. parapertussis does not arise as a mutation, as you claimed. It's always been there - just in a "latent" form until the dominant B. pertussis is eliminated.
Think of your garden. If you eliminate one weed, an opportunity is created for other, less aggressive weeds to flourish. The less aggressive weeds are not mutations, created by you when you kill the more aggressive weeds. You just created an opening for other weeds.
It's a similar idea with pertussis and parapertussis. The vaccine is like a herbicide. Then the dominant B. pertussis "weed" dies off, the less aggressive B. parapertussis springs up.
Joanna, I know you fancy yourself a science writer. Here's an opportunity for you to adjust your belief to new evidence. It's what scientists, and science writers, do.