"Desire" implies that the bacteria is acting purposefully and planning ahead. This isn't what's happening unless you attribute the bacteria's activity to some sort of intelligence.
On the contrary, we eliminated smallpox which was one of the most devastating diseases in history so this fatalism is basically disproved. More depressingly, we've also made extinct thousands of species who have not evolved to resist us.
That comment digressed to discuss whether or not evolution plans ahead and "eventually discovers ways to overcome" as implied by the OP. Keep up with the topic :)
The bacteria is acting purposefully I guess in the same sense that a hammer acts purposefully to drive down a nail. I don't know if that's a correct usage of language or not but it's essentially the same thing. But it is correct to say the hammer's purpose is to drive down the nail, and the bacteria's purpose is to survive and reproduce successfully.
So what if a species goes extinct? That doesn't mean it can't evolve, only that it didn't adapt quickly enough.
On the contrary, we eliminated smallpox which was one of the most devastating diseases in history so this fatalism is basically disproved. More depressingly, we've also made extinct thousands of species who have not evolved to resist us.