As swine flu spreads, affecting nearly 6 million Americans by now, spreading fever and discomfort and creating long lines of people waiting for vaccine that's in short supply, reports say that scrutiny of large hog farming operations has slowed down, not speeded up. Virologists and other specialists are alarmed because it's been known for years that workers on these farms are exceptionally likely to show elevated levels of swine flu antibodies.

There are more reasons than one why that fact is disturbing. Cheap meat—low-cost beef, chicken and pork raised on farms so huge that the economics of scale put meat-rich meals within reach of everyone except the very poor—has been the staple of the American diet. The confidence of the carnivorous consumer in meat with the USDA (U.S. Department of Agriculture) logo was almost unbroken for decades until the mad cow disease scandal and the discovery that animal corpses were used as cattle fodder created a market, though hardly more than a niche market, for grass-fed beef raised without antibiotics and growth hormones.

No other scare, except for periodic E-coli outbreaks, has seriously interfered with the year-round pastime of barbecuing, grilling, frying and roasting that makes meat the premier item on the table for most of us. But now comes a swine flu pandemic, and an unwelcome question arises. It is not, as with the beef scares, the question of whether the meat is safe to eat (it is). The question this time is, do the big farms that put cheap pork on our tables increase the risk of infection that can be deadly, especially to children?

What does the average consumer even know about the large, increasingly controversial livestock operations known as CAFOs?

Concentrated Animal Feeding Operation [CAFO] is a legal term for an indoor or outdoor lot or other facility where animals are housed and fed for a total of 45 days in a given year, and where there are no crops or vegetation, including postharvest vegetation such as corn stubble. The important thing about the lack of vegetation is that it means that there is neither anything for the animals to forage on naturally, nor anything to absorb their excrement; labor unions and people living near large outdoor pig CAFOs have complained for years about the tons of excrement that breed clouds of flies, emit odors that have been known to sicken neighbors, and occasionally leak into water supplies. It's a common practice to spray hog waste, without treatment, on fields to serve as fertilizer.

To put CAFOs in perspective, consider that in 1967 there were a million pig farms in the U.S.; in 2002 there were only 114,000, and 57 percent of the nation's swine herd is now produced by four companies. A typical large pig CAFO houses around 2,000 sows. (Iowa, North Carolina, Minnesota, Illinois and Indiana are the major hog-producing states; no farming operation in Massachusetts has over 1,000 hogs, and only four have 500 or more.)

On these very large farms, conditions are ripe for the breeding and transmission of flu viruses, according to Gregory Gray, an M.D. who is director of the Center for Emerging Infectious Diseases at the University of Iowa College of Public Health. "When respiratory viruses get into these confinement facilities, they have continual opportunity to replicate, mutate, reassort, and recombine into novel strains," Gray was quoted as saying in an article published in September in Environmental Health Perspectives. Then, he adds, CAFO workers can pass the virus on to people outside the farms.

The evidence? Three years ago, University of Iowa researchers checked samples of blood from pig farmers, veterinarians and meat processors, comparing them with samples taken from university students and staff. Of the farmers, 17 to 20 percent showed evidence of having been infected with flu, as did 11 to 19 percent of the veterinarians. None of the university students or staff and none of the meat processors did.

An earlier study by Gray found that CAFO workers in Iowa showed 50 times the rate of occurrence of elevated H1N1 (swine flu) antibodies as other state residents. An even more striking finding was that their spouses were also more likely to have the antibodies—25 times more likely—than other people. That strongly suggests that the virus can move from pigs to their caretakers to others outside the farms.

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The new outbreak raises that concern to orange alert. "The thing we're concerned about is if this [novel H1N1] virus gets into pigs and then comes back out of pigs into people," Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota, told the Washington Post.

In April, Mexican officials claimed that an outbreak of flu in which a five-year-old girl died of H1N1 infection was caused by conditions at a large hog farm run by a subsidiary of Smithfield Foods. They could not back up the claim with hard scientific evidence. But data gathered by Gray and other specialists shows that links between swine farms and swine flu are worth investigation.

There is, however, no regular, industry-wide surveillance program for swine flu in animals or workers at hog CAFOs. It's still the case that, as the Wall Street Journal reported in May, the government has embarked on "no extensive sampling program of the sort that is used by the federal government to alert it to other animal diseases, such as mad cow disease and bird flu." Some large operations, like Smithfield Foods subsidiary Murphy-Brown, require workers to get flu shots every year. Late in 2008, the CDC funded a $1.5 million program to search out new strains of flu virus in pigs. But this program will only test animals pig farmers submit voluntarily.

Meanwhile the Washington Post reported late in October that efforts to detect the flu virus have "actually decreased in the six months since the H1N1 strain was discovered in California and Mexico in April." Fewer veterinarians are bringing pigs into diagnostic labs in at least three states, Iowa, Kansas and Minnesota, according to the Post; the Iowa State lab just cut three positions for financial reasons.

On the other hand, last week the U.S. Department of Agriculture announced that the H1N1 virus had been found "for the first time in a commercial swine herd," a herd of undisclosed size in an undisclosed location in Indiana. And six H1N1-infected pigs turned up at the Minnesota State Fair in September. Some might have caught the virus from people at the fair, but Gray says that one had been sampled before being unloaded.

Industry spokespeople say their operations are biologically secure without more aggressive government-sponsored inspection. "There are a number of ongoing monitoring activities that take place on a daily basis. If something unusual is going on, we call our veterinarians and they take it from there," Don Butler, public affairs director for Murphy-Brown, told the Advocate. "I am not aware of any peer-reviewed research that links hog operation to the outbreak of H1N1 in anybody."

Elizabeth Wagstrom, a veterinarian with the National Pork Board, says the H1N1 Gray and his colleagues found in pig handlers is an older strain of H1N1 and "not the novel H1N1" that is causing the pandemic. Gray acknowledged in an email to the Advocate that much of his research was done before the current outbreak of H1N1, as is clear by the dates of his studies—but pointed out that the virus found in the hogs at the Minnesota State Fair, in a sampling project financed by the federal Centers for Disease Control, was the novel H1N1. In earlier research, Gray had also said that contact between pigs and humans, in small farms but especially in large ones where that contact is more intense, might give rise to novel flu strains.

The industry also challenges the suggestion that the very large farms may bear more responsibility for the current outbreak of swine flu than smaller farms where pigs are raised. Wagstrom points to a study published early this year by researchers at the Iowa State University College of Veterinary Medicine that found a 20 percent higher instance of H1N1 in pigs from small herds than in pigs from the larger herds as the latter were described in previously published research. It's important to notice, though, that that study only included animals that were sick to begin with.

At the moment, many hog CAFOs fall between cracks in federal regulations. For example, automatic feeding devices and other technology make it possible for seven workers to tend a couple of thousand hogs, but OSHA (the federal Occupational Health and Safety Administration) rules only require routine worker safety inspections at sites employing 11 workers or more. OSHA has a standard, the Bloodborne Pathogens Standard, to monitor the spread of infectious diseases in workplaces. But the BPS does not apply to respiratory diseases, which so far has put swine flu beyond its reach.

Gray wants some of the large farming operations to be opened to academic researchers. Butler told the Advocate that whether Murphy-Brown might allow studies to be done at its farming sites "would depend on who's doing the asking and what kind of intrusion it might impose on our operations."

It's not clear that hog CAFOs are the breeding grounds and transmission centers for swine flu. What is clear is that the issue deserves more examination. Ellen Silbergeld, an epidemiologist who is a professor at Johns Hopkins University's Bloomberg School of Public Health and a former scientific advisor to OSHA, the Environmental Protection Agency and the World Health Organization, has noted that research on so-called zoonotic infections (infections transmitted from animals to humans) has tended to overlook CAFO workers. Silbergeld has received a grant from the National Institute of Environmental Health Sciences to investigate possible relationships between industrial animal production and zoonotic infections.

Meanwhile, workers in pig farming operations need training and protection for their own safety and to assist in preventing epidemics, according to Gray. In "Facing Pandemic Influenza Threats: The Importance of Including Poultry and Swine Workers in Preparedness Plans," published last year in Poultry Science, Gray and another University of Iowa epidemiologist, Ghazi Kayali, point out that sick pigs have been shown to be infected with viruses with human genetic components. People who work with swine, they warn, "have potential to act as 'mixing vessels' from which new strains of influenza viruses can emerge," and as "bridges" through which infection can reach humans. They urge that these workers be at priority to receive vaccines, and be trained to minimize the spread of infection to their families and others beyond the farms.