The thing I've talked about with other people, is that possibly where the aliens are from, they had no bacteria, or completely exterminated all bacteria many years ago.
So when they wanted to invade, they never bothered trying to look for bacteria, because they had no idea what it was.
Another theory, is that when they planted the tripods here "millions of years ago", they found our bacteria, and came up with a solution to fight it. Now though, many years in the future, the bacteria has mutated and evolved so that they are no longer immune to it.