"As a general principle, the concentration of humans or animals in proximity enhances potential transmission of microorganisms among members of the group. It also creates greater potential for infecting surrounding life forms, even those of different species. The conditions created also may be a breeding ground for new, more infectious, or more resistant microorganisms." (Gilchrist 2006)
Concentrated Animal Feeding Operations, or (CAFOs), also called confined animal feeding operation, are large farms with massive amounts of swine, cattle, hogs, or other animals. The high density of stock is where the name comes from. Although they're very economical, recent studies have shown that CAFOs have increased the risk of Nipah virus infections and Avian influenza not only infecting animal populations, but also causing zoonosis, diseases being transferred to humans from animals. "The rural and agricultural community has changed dramatically over the past half century. The trends include an overall reduction in the number of farms, an increase in size of the farms, and economic concentration in the industries that supply inputs and purchase commodities from farms." (Donham 2006)
At this level, bacteria is increasingly becoming resistant to antibiotics. "Escalating resistance has raised concern that we are entering the “post antibiotic era,” meaning we may be entering a period where there would be no effective antibiotics available for treating many life-threatening infections in humans." (Gilchrist 2006) CAFOs don't even use high levels of antibiotics. That's the problem. They use antibiotics in low levels not for bacteria protection, but for a 4-5% increased growth in the animals, as well as an increase in food turnout.
"This prolonged use of antibiotics, especially at low levels, presents a risk of not killing the bacteria while promoting their resistance by selecting for resistant populations. The resistance genes can pass readily from one kind of bacteria to another (Levy 1998). Thus, workers in the animal units may become colonized with resistant organisms and can pass them on to co-workers and family members or friends. Consumers of meat may also become colonized through mishandling of raw meat or through insufficient cooking. Ultimately, these genes may pass into pathogens, and diseases that were formerly treatable will be capable of causing severe illness or death (NAS 2003)." (Gilchrist 2006)
Ecofeminists (among other groups) argue that life confinement for these animals is unethical. Where "farm animals" would at least get hay to sleep on, factory farm animals are sometimes required to sleep standing in stalls, so that its easier to clean for workers. Ecofeminists also go further in their arguments against CAFOs saying that they are just as unjustifiable as rape of a woman. We are raping Mother Earth.
Gilchrist 2006 (The Potential Role of Concentrated Animal Feeding Operations in Infectious Disease Epidemics and Antibiotic Resistance, Journal List > Environ Health Perspect > v.115(2); Feb 2007)
Donham 2006 (Community Health and Socioeconomic Issues Surrounding Concentrated Animal Feeding Operations, Journal List > Environ Health Perspect > v.115(2); Feb 2007)