Sci-fi movies may portray zombies or aliens taking over the planet, but what about bacteria? They are proving to be a very clever group of microorganisms, and our prolific overuse of antibiotics is making the bugs increasingly stronger as they outsmart attempts to fight them. Will they be our undoing?!

In few places is this more apparent than in our food system which seems to be breaking down in alarming ways, as evidenced by an estimated 48 million cases of foodborne illness occurring each year in the U.S. And in fact, a new report by Environmental Working Group details the problems that widespread use of antibiotics in animals causes for humans. (Read all about it here: Antibiotic-resistant bacteria in meat on the rise.)

Ever since the stunning 2011 recall of ground turkey by Cargill, when 36 million pounds of ground turkey tainted with antibiotic-resistant salmonella killed one person and sickened 136 others, turkey burgers have been in the spotlight. After that incident, the company closed the plant to make it safe. But within a month of reopening, they recalled another 108,000 pounds of ground turkey infected with the same superbug salmonella from the same plant. You just can't keep a good superbug down.

So it is of little surprise that Consumer Reports decided to take a closer look at ground turkey. What they found is rather unsavory.

In their lab analysis of ground turkey bought at retail stores nationwide, they discovered that “more than half of the packages of raw ground meat and patties tested positive for fecal bacteria. Some samples harbored other germs, including salmonella and staphylococcus aureus, two of the leading causes of foodborne illness in the U.S. Overall, 90 percent of the samples had one or more of the five bacteria for which we tested.”

Sixty-nine percent of ground turkey samples tested positive for enterococcus, and 60 percent harbored Escherichia coli. Both are associated with fecal contamination.

Adding to the bacteria-will-one-day-rule-the-world scenario, the report says that all of the disease-causing organisms in the 257 samples proved resistant to one or more of the antibiotics commonly used to tackle them. About 80 percent of the enterococcus bacteria were resistant to three or more groups of antibiotics, as were more than half of the E. coli.

Why? Because factory farms are very liberal with their use of antibiotics. Bacteria that are immune to their effects flourish and spread, and often exchange genetic material with other bugs, becoming stronger and accelerating their antibiotic resistance.

Mother Jones reports that between 2003 and 2011, antibiotic use on US livestock farms rose from 20 million pounds per year to 30 million pounds - a stunning 50 percent increase. “These facilities now suck in 80 percent of the antibiotics consumed in the United States,” they note. “The great bulk of these drugs are used not to treat sick animals, but rather to make them grow faster and keep them alive until slaughter under tight, filthy conditions.”

So rampant is the problem that Consumers Union, the advocacy arm of Consumer Reports, says that the FDA should ban all antibiotics in animal production except to treat illness.

The only part of the story resembling good news is that although ground turkey labeled “no antibiotics,” “organic,” or “raised without antibiotics” was as likely to harbor as much bacteria as factory farmed turkey, at least the bacteria found on these products were much less likely to be antibiotic-­resistant superbugs.

If you're still a turkey-burger eater after reading this, the following tips may offer some guidance.

  • Buy turkey labeled “organic” or “no anti­biotics.” The “USDA Process Verified” label indicates that the USDA has confirmed that the producer is following the guidelines.
  • Labels that say “animal welfare approved” and “certified humane” mean that antibiotics were only used on sick animals.
  • A label that says “natural” means that it was minimally processed and contains no artificial ingredients or added color, but it doesn’t preclude the use of daily antibiotics.
  • At the supermarket, pick up meat just before checking out and place it in a plastic bag to prevent leaks.
  • If you will cook meat within a couple of days, store it at 40F or below. Otherwise, freeze it.
  • Follow the federal food safety guidelines to clean, separate, cook, and chill.
Or, skip the bird altogether and try one of these 10 veggie burger recipes instead.

Related foodborne illness stories on MNN:

Nearly 70% of turkey burgers contain fecal bacteria, says Consumer Reports
Overall, 90 percent of the ground turkey that the magazine examined had one or more of the five bacteria they tested for.