On our bodies live bacteria and viruses that we refer to as "normal flora" and with whom we happily coexist. When humans interact with a new organism for the first time, either our immune systems kill it, or it kills us. Neither of these situations benefits an organism, because by killing its host it's lost its place to live. Over time, microorganisms have evolved alongside humans so that they can reproduce in and spread human-to-human, and so that they can live in their hosts for a long time. Thus, our normal flora are creatures that don't harm us.
Except: some pathogens are normal flora organisms that have escaped from where they are supposed to live on our bodies (the surface of our skin, the inside of our gut, etc.) and found residence in tissues where they do harm us. Human influenzae type B (HiB), a bacterium for which we have a vaccine, is an example of this.
So it occurred to me that these normal flora with pathogenic capacity are probably at an evolutionary disadvantage to their normal flora compatriots without pathogenic capacity. They are slowly killing off their hosts faster and thus wiping themselves out relative to other bacteria and viruses. That means that we are studying a set of pathogenic normal flora that exist at a unique moment in history: there may have been others before that wiped themselves out; this set we have now would eventually wipe itself out if left to its own devices.
But then, we vaccinate against some of these pathogenic normal flora: this doesn't mean that we don't have HiB on our bodies anymore, only that we have it still and that it can't make us sick. So, in a way, aren't we ensuring its longevity in the population with our vaccine? (Note: not all vaccines are against normal flora. Other vaccines can essentially wipe out an organism by making sure that its only host, humans, can always kill it. Smallpox was eradicated through vaccination.)
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