During the sceen at the ferry crossing, when we first notice the tripods coming, at first I thought the birds were flying away from it. When the tripod becomes visible, we see the gulls flocking around it. Now, birds are one of the worst carriers for parasites and bacteria (salmonella for one). My thought is that the birds were attracted to the red weed stuff the tripods were spraying (terraforming?) and they they may have spread disease to the aliens that way. There is also the sceen in the basement where the aliens are shown drinking the water from the drain pipes, which after all the damage that they had wrecked, probably wasn't clean anymore. I think that Speilberg left it open for a number of ways of infecting the aliens.