What to Know About Antibiotics and Antimicrobial Resistance

Chasing away an infection with the right antibiotic can feel magical.

Stabbing throat pain improves, coughs subside, ear aches fade. A course can save us from pneumonia and protect us during surgery. The advent of penicillin has been hailed as one of the greatest discoveries in medicine.

But an antibiotic can also be a temptress. While the drugs work by killing or inhibiting the growth of bacteria, we often seek them out for runny noses and chest colds, most of which are caused by viruses. An estimated 28 percent of antibiotics prescribed to children and adults are unnecessary. When a virus like those that cause the flu or Covid is causing your symptoms, antibiotics not only don’t help, they can hurt.

Swallowing an antibiotic is like carpet-bombing the trillions of microorganisms that live in the gut, killing not just the bad but the good too, said Dr. Martin Blaser, author of the book “Missing Microbes” and director of the Center for Advanced Biotechnology and Medicine at Rutgers University. Drug-resistant bacteria are already in all of us; beneficial bacteria help keep them controlled. When an antibiotic wipes out beneficial bacteria, the resistant bugs can flourish, making present and future infections harder to treat. With the overuse of antibiotics, our microbes are disappearing, a crisis with far-ranging consequences scientists don’t fully understand yet. “I think the health profession in general has systematically overestimated the value of antibiotics and underestimated the cost,” Dr. Blaser said.

Antimicrobial resistance is one of the top global public health threats, according to the World Health Organization. Each year in the United States, an estimated 2.8 million antimicrobial-resistant infections occur, leading to more than 35,000 deaths. If you take a lot of antibiotics, you are at greater risk of developing an antibiotic-resistant infection and spreading it to others. That can contribute to the rise of antibiotic-resistant bacteria, sometimes referred to as superbugs. To top it off, taking antibiotics regularly may also make you more susceptible to other illnesses.

Antibiotics also disrupt the good gut bacteria that are responsible for helping with metabolism, digesting food and educating the immune system. Researchers are currently studying whether this can lead to metabolic disorders, such as Type 2 diabetes, and autoimmune diseases. Research in animals suggests it does lead to chronic diseases. The data suggest this is true for humans, too, said Dr. Lauri Hicks, director of the C.D.C.’s Office of Antibiotic Stewardship, but the link between antibiotic use and different chronic diseases requires further study.

In recent years, experts have been pushing for an overhaul of the way we use these medicines. “This is a mindset,” said Dr. Sara Cosgrove, professor of medicine in the division of infectious disease at Johns Hopkins University School of Medicine. “You do have to get yourself out of the traditional — to some degree, American — mindset that antibiotics are always good and don’t cause harm.”

Here are a few tips on how to have an open conversation with your doctor about antibiotics.

Find out if you really need an antibiotic.

So your doctor suggests an antibiotic. “Say, ‘OK, doc, what are we treating here?’” recommends Dr. Jeffrey Gerber, associate professor of pediatrics and epidemiology at the Perelman School of Medicine at the University of Pennsylvania. Get a clear understanding of which bacterial infection the antibiotic is targeting. Ask if there’s a test to ensure that the medication is indicated and whether you can wait a few days to fill the prescription if you’re not improving.

“A little skepticism is needed,” said Dr. Emily Spivak, an infectious diseases doctor at University of Utah Health.

Also inquire which medication has the fewest side effects. Adults and children routinely go to the emergency room because of problems that arise from taking antibiotics. A broad-spectrum antibiotic, which is capable of fighting many different types of bacteria, can kill off more good bacteria and generally has more side effects, like diarrhea. This type of medication can also lead to more antibiotic resistance, although there are times when it may be the right treatment. Your physician or pharmacist can explain what kind of antibiotic is being prescribed and also tell you if a narrow-spectrum option might work.

Whatever you do, don’t ask for an antibiotic: Research suggests that doctors are more likely to prescribe the medication when they perceive patients expect it.

Ask for the shortest course.

It was long believed that if you didn’t finish the whole course of antibiotics, the bacteria might become resistant. But evidence has emerged that the longer you take antibiotics, the more likely you are to be susceptible to another bacterial infection. “After minimizing the biological costs of antibiotics for decades, medical scientists are finding evidence that longer courses are more damaging than shorter ones,” said Dr. Blaser, who was not involved in the new research. “This will change how we approach the length of treatment in the future.”

Research has also started to show that shorter courses of antibiotics for some conditions can be just as effective as longer ones. When Dr. Blaser started out in medicine, he said, physicians would usually treat a simple urinary tract infection with a two- to three-week course of antibiotics. Now it can be three days or less.

The American College of Physicians recommends shorter courses of antibiotics to treat common bacterial infections, such as community-acquired pneumonia. Most cases do not require antibiotics for longer than five days.

For most children, the recommended antibiotic course for a sinus infection has been cut in half, and is now 5 to 7 days; it’s similar with community-acquired pneumonia, according to the American Academy of Pediatrics.

Yet some doctors still prescribe the longer courses. If that happens, Dr. Hicks recommends respectfully asking if you need to take the full course.

Prolonged treatment may be needed for chronic or recurrent infections; a specialist can help make the determination, Dr. Blaser said.

Some experts suggest asking whether you can stop your antibiotics if you’re feeling better. “Some patients are going to have rocket immune systems, and be young and healthy, and they might be better after just a couple days,” said Erin McCreary, a pharmacist and director of infectious diseases improvement and clinical research innovation at UPMC.

Rethink probiotics.

Often doctors will recommend taking a probiotic in conjunction with an antibiotic, in order to ease some of the associated diarrhea and with the idea that it can help restore the microbiome’s array of good bacteria. But Dr. Blaser said the jury is still out: Some findings suggest that probiotics may possibly prolong the time it takes for the microbiome to return to its pre-treatment state. There’s some evidence that probiotics may help prevent antibiotic-associated diarrhea, though it’s not conclusive, said Hye-Sook Kim, a program director who oversees microbiome and probiotics research at the National Center for Complementary and Integrative Health.

Probiotics may reduce the risk of developing the life-threatening infection Clostridioides difficile, which can cause severe diarrhea and inflammation of the colon, called colitis. It’s usually caused by exposure to antibiotics; those who take them more frequently are at greater risk.

For the majority of people, Dr. Spivak said probiotics are “fine to take, I just can’t guarantee it’ll make any difference.”

If you are going to take them, you might do so after finishing your medication. “Practically speaking, it’s spitting in the wind to take them simultaneously,” since an antibiotic can kill the good bugs in a probiotic, said Dr. Neil Stollman, a gastroenterologist at Alta Bates Summit Medical Center in Oakland, Calif., and a fellow of the American College of Gastroenterology.

Of course, even the experts who are critical of antibiotic overuse take the medicine sometimes, when really needed. Dr. Blaser himself took a full course after noticing a huge bull’s-eye on his torso, the telltale mark of Lyme disease. And Dr. Cosgrove did, too, after her black cat, Angus, scratched her. “The redness was crawling up my arm,” she said. “Antibiotics were definitely indicated.” A short course quickly cleared it up. Several years later, neither doctor has taken antibiotics since.