Solutions
There are many solutions to the problem of factory faming, the most obvious being shut down the factory farms all together, but this solution would not work because factory farming is far too large and profitable of an industry to shut down. A feasible solution would be to enforce the Humane Methods of Livestock Slaughter Act, and make an amendment so that it applies to birds as well. It shouldn't be difficult for large companies to train their workers to act more humanely towards the animals, and it would increase profits if customers knew a company raised their animals in a humane way, because people don't like knowing they are eating abused animals. We can also create laws stating livestock should have enough room to move, so that they aren't confined to one tiny space their entire lives. Laws can also be made requiring any runoff from farms to be stopped or collected before it infests other places.
Stricter laws can also be put into place regulating what meat can be put on the market, that way meat from infected cows or pigs or chickens is not sold in the market, possibly infecting humans.
Another solution individuals could take would be to either turn vegetarian or vegan, or make sure you buy your meat and other animal products from a free range farm, meaning the animals are free to roam outdoors for at least part of the day, that way they aren't confined indoors 24/7.