A news story making the rounds this week suggested that more than half of the retail samples of ground turkey, pork chops and ground beef tested by federal officials were found to contain antibiotic-resistant bacteria.

In a way, that’s old news, because the data were actually collected in 2011 by the National Antimicrobial Resistance Monitoring System, a joint program of FDA, USDA and the Centers for Disease Control and Prevention. Though nearly two years old now, the data showed a significant increase in the amount of products found with antibiotic-resistant forms of salmonella, E. coli and campylobacter.

The government initially published the findings in February this year, but the release generated little media coverage—until the Environmental Work Group issued a report titled, “Superbugs Invade American Supermarkets.” What’s important to know about that report—other than its provocative title—is that a company called Applegate helped underwrite the report. Good company, excellent products, but an organization with an agenda, since Applegate markets organic and antibiotic-free “natural” meats.

Although EWG representatives raised the red flag—“The numbers are pretty striking,” said Dawn Undurraga, a nutritionist with the health advocacy organization—veterinarians working with work with such groups as the International Food Information Council and the U.S. Farmers and Ranchers Alliance criticized the report, calling it “misleading.”

“The No. 1 misunderstanding about antibiotics in animal agriculture is that it is not understood well enough that antibiotics are used to keep animals healthy, period,” Randall Singer, a veterinary science professor at the University of Minnesota, told The New York Times.

There are problems with the methodology of the government survey, Singer argued. He noted the limited number of samples in the data—480 samples each of ground turkey, pork chops, ground beef, chicken breasts, wings and thighs—is tiny compared with the amount of meat sold in the United States.

But he voiced a more serious charge, one at the heart of the animal antibiotics debate, in saying, “We should not assume that when we find resistance to antibiotics in humans, it means it was caused by the use of antibiotics in animals.”

No, we should not. But we also shouldn’t rule it out a priori, either.

A bowl of bacteria

Here’s another factoid that media members rarely separate out from an overall focus on the idea of “contamination!”

By far, the most contaminated product samples were poultry, not beef or pork, with data indicating that raw chicken tested positive for coliform and enterococcal bacteria on between 94% and 99% of samples—almost every single sample.

But that shouldn’t be surprising. Have you ever seen the chill tanks in a poultry plant? After every chicken or turkey carcass is dunked in the industrial equivalent of a giant bowl brimming with bacteria, No matter what its bacterial status might have been at the beginning of production, they end up contaminated.

I mean, here’s the procedure the scientists used to prepare the supermarket samples for testing: “Samples [of chicken turkey or pork chops] were placed in separate sterile plastic bags with 250 ml of buffered water, then the bags were vigorously shaken. [Then] 50 milliliters of the rinsate from each sample were transferred to individual sterile containers for bacterial isolation.”

That’s pretty much how poultry is handled following de-feathering and evisceration in a typical processing plant.

Ground turkey was equally as contaminated as chicken, for identical reasons—plus the added benefit of mixing, grinding and blending mountains of trim, skin and mechanically deboned meat together in 5,000-lb. mixer/grinder/blenders. If there were any bacteria present in any of the turkeys, by the time the ground product is ready for packaging, well, if there’s a better way to uniformly distribute bacteria, I’d like to know what it is.

Those in the industry understand that animals grown for meat are fed diets containing low-level antibiotics to promote growth, improve efficiency and prevent illness. That’s a net positive, and countries such as Denmark that have eliminated sub-therapeutic use of antibiotics have found increased morbidity, increased levels of respiratory and other diseases and a consequent increase—not decrease—in the use of stronger doses of second- and third-generation antibiotics.

Despite what certain industry apologists want everyone to believe, that may well be a causative factor in the increase of antibiotic-resistance among some very nasty human microbial pathogens. It’s not the only factor, nor even the most significant one—it stands to reason that overuse of antibiotics in hospitals, where the drugs are administered directly to patients—would be a far more important variable.

Meanwhile, a growing awareness and concern about antibiotic resistance is fueling an increase in sales of antibiotic-free meat, like the products Applegate sells.

The FDA has recommended that farm use of antibiotics be limited to uses “considered necessary for assuring animal health.”

That might not be a bad end point, especially if approached voluntarily, and industry ought to consider how to get there from here.

The opinions expressed in this commentary are solely those of Dan Murphy, a veteran food-industry journalist and commentator.