My mistake. Animals are stuffed with antibiotics but you're right that swine and bird flu are caused by viruses. This article explains why factory farming is dangerous with regards to bird flu:

> The conditions on these farms greatly contribute to the creation of deadly pathogens, including influenza viruses. Here’s how it works: Wild aquatic birds are the primordial source of all influenza A viruses — the ones that have the potential to cause pandemics. However, people rarely become infected directly from aquatic birds. Usually, an intermediate host must be involved. This intermediate host provides the right biological setting for the virus to transform into something that can easily infect a human. And that’s where chickens and other farmed animals come in.

Most avian influenzas are mild, low-pathogenic (i.e., not very lethal) viruses. However, once they enter poultry factory farms (through insects or workers carrying the virus, for example), they can rapidly mutate into highly-pathogenic (very lethal) viruses, even over very short periods of time. Since 1990, outbreaks of highly-pathogenic virus subtypes have increased substantially among farmed birds compared with the years prior to 1990 (3, 4). The intensive confinement of birds has been found to facilitate both the increasing frequency and scale of these outbreaks (3, 5).

http://www.huffingtonpost.com/aysha-akhtar/bird-flu_b_279813...