A study published last week in the journal Clinical Infectious Disease found that Iowa pig farm workers were six times more likely than non-pig farmers to carry multi-drug resistant Staphylococcus aureus (S. aureus). Non-therapeutic use of antibiotics is the likely culprit.

The presence of antibiotic-resistant bacteria is a growing problem, as doctors find it increasingly difficult to deal with ever-hardier critters, some even being dubbed “superbugs.” One such super-bug, Methicillin-resistant Staphylococcus aureus (MRSA) attacked my roommate a few years ago.

On her face.

It started as what she thought was a pimple on the bridge of her nose, but she quickly realized something else was up.

“I woke up and the thing had practically exploded.” She described to me, remembering the infection at its worst–a painful, throbbing, nickel-sized abscess, stretching her skin to the point of cracking.

“It was like a little baby pus alien, pushing its way out of my face. . . Pretty heinous.” She said.

She ended up with some hefty hospital bills, a faint red spot on her nose, and a plush MRSA microbe doll, complete with its “superbug” cape (my attempt at a gag/get well gift).

She was lucky. A 2013 CDC report attributes more than 2 million illnesses and over 23,000 deaths to drug-resistant bacteria. Resistance pops up in places like hospitals, due in part to doctors prescribing unneeded antibiotics, or patients not properly completing their assigned dosage. The report cautioned: “Simply using antibiotics creates resistance. These drugs should only be used to treat infections.”

But some of the most serious misuses of antibiotics occur on the farms that produce our pork chops, steaks, and eggs. In fact, a vast majority of antibiotics in this country are consumed by animals, instead of humans. In meat production antibiotics are often used not to treat infections, but rather in a prophylactic attempt to prevent infection in the first place, or as a growth promoter.

The public health threat posed by non-therapeutic antibiotic use in agriculture led the FDA in 2013 to establish guidelines on antibiotic use in meat production (read Wired‘s Maryn McKenna and Grist‘s Nathanael Johnson for great reporting on this topic). I spoke with Dr. Jennifer Koeman of the National Pork Board (NPB) about the recent Iowa study, as well as the pork industry’s response to the FDA’s 2013 recommendations.

She told me the NPB is embracing the guidance. “Antibiotic use and resistance in the pork industry has been a focus for several decades,” she said. Koeman told me that one of the practices promoted by the industry’s Pork Quality Assurance Plus program is the responsible use of antibiotics. She also pointed out that the increased colonization of drug-resistant bacteria among swine workers does not necessarily translate to increased infections.

Tara Smith, one of the authors of the Iowa swine farmers study explained that while they weren’t able to demonstrate a direct link between the colonization among workers and specific infections, “We do know that being colonized by Staph aureus is one of the leading risk factors for infections.” She also told me that these things are difficult to study, and that the pork industry wasn’t exactly making researching antibiotic resistance any easier.

“In the decade that I’ve been doing these studies, it’s been much harder to work with industry on this.” Smith said. She told me that recent legislation aimed at groups like PETA, so-called “ag-gag” bills, have even had a chilling effect on public health research. She and her colleagues have found it increasingly difficult to get access to farms in order to effectively study the effects of non-therapeutic antibiotic use on antibiotic resistance.

Smith told me that despite industry assurances of best practices in the use of antibiotics, the problem is accountability and transparency. “We don’t even know what is going into the pigs in our back yard. . . I’m not sure why they’re unwilling to provide that information,” she said, pointing out that it would be much easier to verify responsible use if the industry were more open to working with independently funded researchers.

Eric Kriedermacher runs Pork and Plants, a farm in southeastern Minnesota, where he raises pigs without antibiotics. He grew up raising pigs, inheriting the farm from his father. Just like so many other farmers, there was pressure to produce large numbers of pigs in conditions that were controlled, but not exactly pleasant for the animals.

He told me he originally had about 1,200 pigs in a 44′ X 96′ barn (roughly 3.5 square feet per pig). “They were housed in their own excrement and never saw an ounce of sunlight. It was a much more controlled environment, every element [humidity, temperature, etc.], but when I was in that world, it just wasn’t working.” He said pigs were sick all the time, and a steady input of antibiotics was par for the course.

Things changed for him, he told me, when he started a family.

“I didn’t want to feed them that stuff.” He said. “I never bought pork off the supermarket shelf because my whole life I knew how it was raised.” Instead, starting with three pigs to feed his family, he began a pasture raised, outdoor system that grew and eventually replaced his indoor system, as word spread among friends and neighbors about the operation.

“We never gave them antibiotics. It took me a few years to convince even my own family that you can raise pigs and chickens without antibiotics. . . But there was no comparison. My pigs are outdoors, they’re never sick, we give them pasture, we give them sun, and we give them green.”

While the U.S. pork industry has yet to embrace systems like Kriedermacher’s, Denmark ended antibiotic use in the 1990s. The result has been largely successful. The cost of raising a pig did rise by about EUR1, but reports show that resistant bacteria have decreased, and productivity and efficiency have increased.

So does the U.S. need a wholesale shift to only small-scale farms like Kreidermacher’s? Tara Smith doesn’t think so.

“It’s not dichotomous,” she said. “I think you can still raise pigs on an industrial scale, but our current methods aren’t conducive to doing it without antibiotics. Small tweaks like nursing the pigs longer or giving them more space can help reduce the need for antibiotics.”

Perhaps one of the barriers to these tweaks is our insatiable appetite for large portions of cheap meat, available at nearly every meal. I asked Smith about what needs to change.

“I think it’s something consumers are thinking about more and more. . . Even if your legislator can’t do anything about it, you can vote with your wallet, and the industry pays attention to that. Whenever you can, choose meat that’s been raised without antibiotics–locally, and sustainably.”

Major chains like Chipotle, Panera, and even McDonald’s have recently undertaken drastic changes to their menus in response to consumer demands. While some of these are based on misinformation or unfounded fears, the threat of antibiotic resistance is real, science-based and could affect us all.

If consumers start giving this issue the attention it deserves, maybe fewer people will end up with pus aliens burrowed in their faces. If we start paying attention to antibiotic resistance, eat better meat, and less of it, we can all help stop the pus aliens.