Much of the contentious debate over the abuse of antibiotics in farming boils down to a couple of simple questions: whether resistant organisms that arise on farms because of antibiotic use leave the farm, and whether, once they do, they reach human beings.

A piece of research (PDF) released Friday morning in the journal Clinical Infectious Diseases helps answer both those questions.

A team of researchers from Arizona bought meat and poultry in five cities across the United States, tested them for bacteria, and found this: 47 percent of the samples contained the very common pathogen Staphylococcus aureus, and 96 percent of those isolates were resistant to at least one antibiotic. Of more concern: 52 percent of those staph isolates were resistant to at least three antibiotics that are commonly used in both veterinary and human medicine.

That is, roughly one in four packages of meat and poultry from across the United States contained multidrug resistant staph.

Here are the details: A team from the Translational Genomics Research Institute in Flagstaff, Arizona, led by Lance B. Price, Ph.D., bought 136 packages of ground beef, chicken breasts and thighs, pork chops and ground pork, and ground turkey, under 80 brand names, in 26 supermarkets in Flagstaff, Chicago, Fort Lauderdale, Los Angeles and Washington, DC. They analyzed the meat for the presence of staph, because staph has been found in the past in several food-animal species. They did a second round of testing to define which strain of staph was on the meat, and then they did a third round, testing the isolates against five important classes of antibiotics, to see whether the staph they had found was resistant.

Which it was. Very. The antibiotics to which the staph was resistant included: penicillin and ampicillin; erythromycin; tetracycline; oxacillin, the more modern form of the drug methicillin; the drug combination quinupristin/dalfopristin, known as Synercid; the fluoroquinolones levofloxacin (Levaquin) and ciprofloxacin (Cipro); and the last-resort drugs for very serious staph infections vancomycin and daptomycin. One staph isolate was resistant to nine different antibiotics.

Among the types of meat tested, turkey carried the most resistance, with 77 percent of the meat samples showing at least some; that was followed by pork (42 percent), chicken (41 percent) and beef (37 percent). Interestingly, it wasn’t all the same staph. Though there was a great diversity of staph types, each animal species seemed to carry mostly one sequence type or strain of staph: ST1 in pigs, ST5 in chickens and ST398 in turkey. (More on that below.)

I spoke to Lance Price about his team’s work. “This is the first study to show that antibiotic-resistant staph is highly prevalent in the American food supply,” he told me.

He added: “There’s an important second point: We found that each of the meat and poultry types had their own distinctive staph on them. That provides strong evidence that food animals were the primary source of the resistant staph. The source wasn’t human contamination of the meat at slaughter, or when it was packaged for retail sale.”

How much resistant staph is present in food animals and on the meat they become has been an urgent question for about seven years, since a team of Dutch researchers identified an unusual staph strain—MRSA ST398—in a family who operated a pig farm. That strain has since spread to pigs across the European Union and into Canada, and has been found to cause human illness in all those areas. It’s also been found in pigs in the United States, though it has not yet been proven to cause human illness here. (I’ve been covering ST398 for several years, and a long archive of posts is available.)

“I think this extends [our work] and opens up some new lines of investigation,” Tara Smith, Ph.D., an assistant professor of epidemiology at the University of Iowa and head of the team that identified MRSA ST398 in US pigs, told me. “The research showed the ‘pig’ strain, ST398, in poultry products, and an especially high percentage of the turkey products. Why is that? Where’s it coming from, and if it’s on the farms, how is it moving between species? Or has it been in these animals for a while?”

And here is where this new finding gets especially complex. The United States has a surveillance system that tests for the spread of antibiotic-resistant bacteria, including in meat animals and food. That surveillance system doesn’t look for MRSA, and in the past few years, because of those pig findings, there has been a lot of pressure to add MRSA to the list.

But even if we did perform nationwide testing for MRSA in meat, that would not have found the multi-drug resistant strains revealed in Price’s work today — because most of them were not MRSA.

What defines MRSA, technically, is resistance to a class of antibiotics known as the beta-lactams, of which the earliest version is methicillin (the “M” in MRSA) and the most common current one is oxacillin. These meat samples, hazardous as they are, were mostly not resistant to oxacillin—and thus a test for MRSA, if we had created one, would have let them slip through.

“We’ve carried out similar testing (unpublished as yet),” Smith told me. “And our results are similar, so it’s not surprising. I do think we need to cast a wider net and not focus only on MRSA.”

People who treat humans tend to dismiss non-MRSA (the technical term is MSSA, for methicillin-sensitive staph) as being no big deal. Price thinks that would be a mistake. He pointed out that several of the strains they found, especially ST1 and ST5, are already known to cause disease in humans.

“You look at these strains and you see they are multi-drug resistant,” he said. “Say someone got infected with one of these, and was treated with oxacillin because it is MSSA, and it developed resistance and became MRSA. That would create a really scary strain.”

So, what’s the risk here? These strains of staph are not the kind that causes food poisoning; their favored spot is not our guts, but our skin and other warm, damp salty places on our bodies, where they can live without causing illness for an unpredictable period of time. So, the issue is not that we will bring the meat home, eat it and develop drug-resistant illness. Instead, it is that we will bring it home, handle it badly and transfer that staph—and its mobile resistance factors capable of moving into other bacteria—onto our bodies and into our homes.

“We know already that most food-borne illness occurs not because of undercooked food” in which pathogens survived, Price said. “It’s from mishandling in the kitchen and cross-contamination. I think there is a risk of these strains contaminating a local environment. We don’t know what that risk is, because it has never been evaluated — but anyone who dismisses that risk is doing so without any data.”

Price’s research was partially funded by the Pew Charitable Trusts, which several years ago supported a massive investigation and report on the impact of antibiotic overuse in agriculture, the Pew Commission on Industrial Farm Animal Production. Shelley Hearne, managing director of the Pew Health Group, told me, “The bottom line is, the more we use antibiotics in injudicious ways, the more we are compromising our ability to save human lives in the future.”