I used to be a field microbiologist, before I went to grad school for engineering. My previous corporate job was development work on a sterilization system used for, among other things, sterilizing anthrax-infected post offices, Salmonella-contaminated food processing plants, BSE-contaminated slaughterhouses and army bioweapons decontamination. So, I think I know a little bit about infection control in the field.
The first thing to know is, what is the source of contamination. For poultry, this could be anything from migratory birds to backyard chickens to poultry received to a factory farm to workers themselves bringing a flu virus into a facility. Other associated sources of contamination include feed, insects in the building, water sources, waste treatment processing and the interior plumbing of the building.
You can't control the migratory birds no matter how much you'd like to.
You might be able to control the neighbor's pet ducks, sort of.
You can definitely control the animals received by the factory farm, which could be upwards of hundreds per day. That requires a full-time vet on site, and probably a full-time diagnostics lab on site. That's expensive. Most guys in suits don't want to hear that they need to deal with increased operating costs for as long as they wish to stay in business.
You can definitely control the workers coming to work sick, but in order to do that you need to have basically unlimited paid sick days and hire only documented, legal workers who pass a medical exam, and have a company nurse on site every hour that the building is open for business. Again, that's expensive.
You can definitely control the feed by doing quality control testing of each batch of feed that enters the building. You can definitely control the water sources and interior plumbing by the same method, just sample the water monthly. Again, you're looking at expensive testing to add to the overhead budget. And if a test comes up as positive for some type of pathogenic bacteria, the costs of shutdown, draining and sanitizing the plumbing and feed equipment are not trivial. Think a few million for the average factory farm. And how are you going to house, feed and water all those animals in the meantime?
You can definitely control the way waste is processed from the plant; however, if your waste treatment (e.g., a waste lagoon outside the building, such as most pig factory farms use) is found to be a source of contamination by harboring disease-bearing insects such as mosquitoes, then you're looking at a steep bill from an engineering contractor to re-engineer your facility from the ground up. Those bills run into the multimillions, in case you're wondering.
Considering that most factory farm operations I've seen are very weak on their own waste processing, insect control, water testing, feed testing and HR sick-time policies, I have my own proposal for the USDA to control zoonotic infections, help preserve family farms (without subsidies or development rights buyouts, imagine that!), improve the genetic diversity of livestock, thus making them more resistant to infections, improve the real estate value of towns where such facilities are located, control foodborne illnesses, improve biosecurity, and improve working conditions for agricultural workers
all in one fell swoop:
Limit the number of animals that can be kept or processed per acre of real estate, so that farming is decentralized amongst several small facilities rather than a few large processors.
Yes, that means economies of scale that currently bring people $1/lb.
Wal-mart chicken will not happen, and chicken and eggs will cost a little bit more. They will NOT cost $10/lb. or whatever the Free Market scare-mongers rant about, and I know this because I can do math, including cost/benefit analysis, too--us engineers are really good at it. If biosecurity and all that good stuff is worth it to America, then it should be worth it to pay $1/lb more for chicken or $0.50/doz. more for eggs
temporarily until the Free Market either adjusts to the inflated cost or else technology finds a way to make a savings elsewhere. Such as, for example, growing feed locally instead of importing it from China, or processing and packaging food on site instead of shipping unprocessed stuff all over the very' place (thereby spreading more disease). Growing local feed and processing food on site has the added benefit of
making more jobs in rural areas that are often impoverished, and preserving green space, for which there are often tax breaks.
Basically, I see NAIS as a cruel joke invented to crap on American jobs and small farmers, which does little for biosecurity. I am not surprised, though, nor do I think it's a plot by the evil gubbermint to get us all: The scientific experts currently informing the government are not field biologists or epidemiologists. They are actually physicists, whose scientific experience is in preventing Cold War era countries from getting nuclear weapons. Since nuclear weapons require plutonium, uranium, etc., things that are relatively hard to get and are best controlled by centralizing their locations, they are following that model of centralizing potential disease vectors. This is not a workable model for biology, though, because the plain hard fact is that pathogens like influenza, anthrax and bubonic plague are literally everywhere--very easy to find in nature, and already spread all over the place. And it's not hard to make something more pathogenic, or to make a transgenic organism; it can be done using your high school student's biology textbook and some household ingredients. Imagine if everyone, literally everyone, had at least one small nuclear reactor in their backyard, complete with instruction manual, and you will see readily that this approach has no hope of success. But that isn't how physicists think, nor is it something they could be expected to imagine.