The problem with animal shelters is that most don't have the resources to observe strict infection control methods. They rely a lot on volunteers who may or may not have any formal training in animal health. My mother rescues small dogs from the pound then places them in homes. We currently have ten dogs, a rabbit, a guinea pig, and one kitten. Four of the dogs are ours, the rest of these critters are available for adoption.
You can not imagine how some of these dogs come into the pounds and shelters. Loaded with ticks and fleas. I mean infested and have actually lost so much blood from ticks and fleas that they're anemic or suffering from tick paralysis. Some are half-starved, ribs showing through, some have been abused, most neglected at the very least and are so starving for attention that it causes them to have behavior problems, some have been fed nothing but table scraps and won't eat dog food.
Its like day care: one child shows up with some bug, starts snotting all over every thing, and all the rest of the children get sick, who then bring it home and give it to their family. Day cares are like little disease factories, so are animal shelters.
One dog shows up infested with fleas, or a cat with an upper respiratory illness, and they're all going to get it. Respiratory illness runs rampant through shelters and pounds. Its a constant battle that most shelters are ill-prepared to fight. And they keep coming, it never stops. Shelters and pounds euthanize tens of millions of unwanted animals a year, try to adopt out what they can, and the unwanted animals still keep coming with no end in sight.