Bats in Nightshade are particularly annoying because they kinda swoop in and take some pretty healthy chunks of your health away when you're not really looking.
But if you've found the whistle, you can totally take care of them. Just find it in your inventory and OPERATE it. It turns out that bats in this game hate the sound it makes.
And they clear out of whatever room you're in
Making it much easier to walk through without the danger of getting rabies.