By Michael Nedelman, CNN

(CNN) -- Our favorite fast foods could come back to bite us, according to a report released Wednesday -- and it's not just the extra calories.

The new report grades the 25 largest US fast food chains on where they stand on antibiotics.

The results are a mixed bag: For the third year in a row, the only two As were awarded to Chipotle Mexican Grill and Panera Bread. More companies passed this year than ever before.

But 11 of the top 25 chains received an F, having taken "no (discernible) action to reduce use of antibiotics in their supply chains."

Nine companies didn't respond to the survey at all, just like last year.

"These drugs have historically been given to animals that are not sick, to accelerate weight gain and prevent disease in crowded and unsanitary industrial farming conditions," wrote the authors, who come from six public interest groups including the Natural Resources Defense Council, Consumers Union and the Center for Food Safety.

While regulations and consumer pressure have encouraged some chains to cut back on the use of antibiotics, some experts worry it's not enough to stave off development of "superbugs" that can't be killed by some of our current medicines. These bugs may get into our meat and produce.

"If we don't rein in this pattern of antibiotic resistance in bacteria, what we will see is half a century of medical progress reversed," said Lena Brook, a food policy advocate with the Natural Resources Defense Council. She has served as a lead expert on the report for each of the past three years.

Despite nearly half of restaurants receiving a failing grade, this is an improvement over the 16 that failed last year, the authors said.

"It's a rapid shift that we've seen in just a few short years, and that leaves me really hopeful," Brook said.

Who passed, and who didn't?

A total of 14 fast food and "fast casual" chains earned passing grades, a boost over nine last year. There were only five the year before that, in 2015.

"It is important to note, however, that while remarkable progress has been made to reduce or even eliminate use of medically important antibiotics, this progress has largely occurred in chicken production," the authors said.

This is how Chipotle and Panera have stood above the rest: by making sure that pork and beef -- in addition to poultry -- are raised without antibiotics.

"While we are pleased to see others in our industry follow our lead in this important area, this report shows that there is still more work to be done across the industry," Chris Arnold, a Chipotle spokesman, said in an email.

The credit for most improved goes to KFC, which jumped from an F last year to a B- after committing to phase "medically important" antibiotics out of its chicken supply by the end of 2018. Antibiotics are considered "medically important" for their use in humans, per the World Health Organization.

Subway earned a B+ for working to curtail antibiotics in poultry and meat. However, its plan to do the same with pork and beef was far off in the future in comparison, keeping it from an A.

Earnings Bs and Cs were Wendy's, Taco Bell and Chick-fil-A. All have made moves to reduce antibiotics in their chicken.

McDonald's also earned a C+, just like last year. The company updated its "Vision for Antibiotic Stewardship" policy in August, saying it planned to pare down unnecessary antibiotic use in all meats. However, the company failed to give a timeline for pork and beef, the new report said.

"We remain committed to making meaningful reductions in the use of antibiotics in beef and pork and will share our progress on beef in 2018," Marion Gross, senior vice president for McDonald's North America supply chain, said in a statement.

Pizza Hut "made a token effort," the report authors said, receiving a D+ for creating policies that affected only a small portion of its chicken. Starbucks earned the same grade for pledging to address antibiotic use in poultry, but not pork or beef.

Earning a D were four chains: Burger King, Dunkin' Donuts, Jack in the Box and Papa John's. These restaurants committed to limiting antibiotic use in some or all of their chicken. However, the companies' plans were unclear or, in the case of Papa John's, unverified by an outside auditor.

So what?

"Antibiotic resistance is one of the biggest health threats facing us today," says CNN Chief Medical Correspondent Dr. Sanjay Gupta. "We've taken too many drugs, and as a result, they don't work the way they used to."

When animals get antibiotics, often in their food or drinking water, the drugs may kill a number of bacteria. But a handful might harbor a gene that makes them resistant to drugs. Those bacteria may survive, multiply and spread.

These bugs "can move off of farms," Brook said, "and find their way into communities." They can even share their genes with weaker bacteria.

The US Centers for Disease Control and Prevention and the World Health Organization have repeatedly warned about the not-far-off public health threat of antibiotic resistance. The CDC estimates that at least 2 million Americans contract antibiotic-resistant infections every year and that 23,000 die as a result.

And these infections are often longer, more costly and more serious, according to the CDC.

The WHO cautioned in a 2014 report: "A post-antibiotic era -- in which common infections and minor injuries can kill -- far from being an apocalyptic fantasy, is instead a very real possibility for the 21st century."

Taking steps

While some experts criticize the routine use of antibiotics, others defend the practice, saying that antibiotics play an important role in maintaining animal health and may prevent an entire herd of sick animals that require these drugs down the line.

Despite the improvements detailed in the new report, Brook said it's unclear why there are so many "holdouts" with failing grades, many of whom did not answer the groups' questions.

"These companies tend to have long-range contracts. Perhaps they're buying from recalcitrant producers," Brook suggested.

With so much variation among the top chains, she said it "points to the real need for federal policy to step in."

The US Food and Drug Administration has taken steps to limit the use of some antibiotics in food animals.

By January, animal drug manufacturers no longer allowed medically important antibiotics to be prescribed solely for growth purposes, according to the FDA. But this left open the possibility that these drugs could be used to routinely prevent disease, even if no animals were sick, so long as a veterinarian had written a prescription.

This drew criticism that the FDA's efforts didn't go far enough.

"This represents a giant loophole in FDA guidelines, which effectively do little to stop the misuse of antibiotics in animal agriculture," the authors of the new report said.

"While the FDA believes the prevention use of antimicrobials in animal agriculture can play an important role in effectively managing animal disease, it is critical that such use be judicious," the agency said in a statement.

The FDA recommends that these drugs only be given if "there are no reasonable alternatives" to prevent disease. It doesn't endorse giving these medications to "apparently healthy animals in the absence of any information that such animals were at risk of a specific disease," the agency added.

"Because (the FDA's) initiative was not fully implemented until January 2017, it is too early to speculate on how this effort may impact antimicrobial use in the animal agriculture setting," the agency said of its plan, which launched in December 2013.

Before the FDA's announcement, around 70% of "medically important" antibiotics were used in farm animals, not humans, according to data by the FDA and QuintilesIMS.

The vast majority of these drugs used in animals are tetracyclines, a class of antibiotics that also includes treatments for chlamydia, Lyme disease and other harmful microbes in humans.

"These are drugs that are really, in plain words, important to the functioning of human medicine as we know it," said Brook.

"What I'm mostly hoping for is that this (report) ... will inspire companies to make similar commitments really quickly."