Medically Approved

From amoxicillin to Z-paks: How doctors choose the right antibiotic for you

5 minute read
A photo of a doctor and patient talking about antibiotics

Learn about the powerhouse medications that fight infections and how to lower your risk for antibiotic resistance.

Amy Marturana Winderl

By Amy Marturana Winderl

Antibiotic medications are among the most important discoveries in modern medical history. Penicillin was the first mass-produced medication to treat bacterial infections. It was called a wonder drug for its lifesaving role in World War II, according to the Microbiology Society.

Since then, scientists have developed more than 100 different antibiotics, including amoxicillin, azithromycin, clindamycin and doxycycline. These medications are used to treat a wide variety of bacteria-related ailments, from strep throat to urinary tract infections. In fact, we turn to today’s antibiotics to solve many conditions that were once considered deadly.

We have so many antibiotics because bacteria are generally good at adapting and surviving. We need to target different types in unique ways to effectively kill them, says David J. Cennimo, MD, an infectious disease specialist and assistant professor at Rutgers New Jersey Medical School in Newark.

“It’s actually very difficult to get a one-size-fits all treatment,” he says. While one antibiotic may be excellent at treating one type of infection, it might do absolutely nothing against another.

That’s because the various types of antibiotics work in different ways, Dr. Cennimo explains. Some break down the cell walls that protect the bacteria. Others disrupt the ability of the bacteria to make the proteins they need to multiply. Still others make it more difficult for the bacteria to copy their DNA. That means the bacteria can’t multiply.

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The antibiotics doctors choose

“Just as every person is unique in their own way, so are the infections they have,” says Michael Richardson, MD, a family medicine physician at One Medical in Boston. So it’s important to take the antibiotic best suited for you and your current concern. Dr. Richardson bases his decision on these factors:

  • Type of infection
  • Severity of the infection
  • Unique needs of the individual (underlying allergies, sensitivities and/or other health conditions)

Antibiotics are grouped into classes based on their chemical structure. Different classes target bacteria in different ways. Here are the main classes doctors prescribe for at-home use, and the ailments they’re typically best at fighting.


Best for: Pneumonia; infections of the ears, nose, throat, gum, urinary tract, respiratory tract and skin
How they work: Prevent formation of the bacteria cell wall
Most often prescribed: amoxicillin, penicillin


Best for: Pneumonia; skin, abdominal, kidney, sinus and prostate infections; plague (it’s still around)
How they work: Prevent bacteria from making new DNA
Most often prescribed: ciprofloxacin, levofloxacin, moxifloxacin


Best for: Bronchitis; pneumonia; Lyme disease; infections of the skin, ears, sinuses, throat, tonsils, bone and urinary tract
How they work: Prevent formation of the bacteria cell wall
Most often prescribed: cephalexin, cefdinir, cefuroxime


Best for: Atypical pneumonias; chlamydia and syphilis; Lyme disease; some types of food poisoning
How they work: Prevent bacteria from making proteins they need to multiply
Most often prescribed: azithromycin, clarithromycin, erythromycin


Best for: Pneumonia and other respiratory tract infections; certain infections of skin, eye, lymphatic, intestinal, genital and urinary systems; some infections spread by ticks, lice, mites and infected animals
How they work: Prevent bacteria from making proteins they need to multiply
Most often prescribed: doxycycline, tetracycline


Best for: Pneumonia; bronchitis; infections of the urinary tract, ears, and intestines; “traveler’s diarrhea”
How they work: These two medications work together to prevent bacteria from making folic acid, which is necessary to make DNA and the proteins it needs to multiply.
Most often prescribed: trimethoprim-sulfamethoxazole, also known as co-trimoxazole


Best for: Infections of the lungs, skin, blood, female reproductive organs and internal organs
How they work: Prevent bacteria from making proteins they need to multiply
Most often prescribed: clindamycin

Urinary anti-infectives

Best for: Urinary tract infections (UTIs)
How they work: Different urinary anti-infectives work in different ways. They either kill bacteria directly, or they prevent them from multiplying.
Most often prescribed: methenamine, nitrofurantoin.

How to prevent antibiotic resistance

We’ve all heard about the rise of infections that are harder to treat. “This leads to the creation of ‘superbugs’ that require more intense antibiotics to finish them off,” says Dr. Richardson. This can happen as a result of taking antibiotics improperly, or by taking them too often.

You can do your part in solving this problem. First, if your doctor says an antibiotic won’t help the condition you have, believe it. Second, always finish your full course of antibiotics, Dr. Richardson says. “Bacteria love to mutate and can develop resistance to antibiotics that don’t fully kill them off.”

If all the problem bacteria aren’t killed off, survivors can surge up again and reinfect you. Over time, this can lead to them becoming resistant to that particular antibiotic. “By finishing your full course of antibiotics, you increase your chances of clearing the infection and preventing the creation of ‘superbugs’ that can wreak havoc on your health,” Dr. Richardson says.

The other way to avoid antibiotic resistance happens at your provider’s office: Your doctor should prescribe antibiotics only when you need them and tailor the remedy to your specific infection. “What drives most physicians’ decisions on antibiotic choice is how selective the antibiotic is against the bug you are trying to treat,” Dr. Richardson says. This will increase the odds of effective treatment.

Common side effects of antibiotic treatment

The dangers of resistance aside, antibiotics are typically safe to take compared to all the other medications out there, Dr. Cennimo says. They may cause rash, dizziness, nausea and yeast infections in some people.

In more serious cases, antibiotics can lead to a bacterial infection called Clostridioides difficile, or C. diff. This infection causes diarrhea and may lead to colon damage. Sometimes it can even be fatal. C. diff develops when a medication kills good bacteria along with the bad. That can mess up the balance of your body’s “microbiome,” or its total population of bacteria. (This imbalance is also what leads to those less-serious yeast infections.)

Antibiotics can also cause severe allergic reactions in some people, and some may interact with other medications you are taking. That’s why it’s always important to talk with your doctor or pharmacist about the drug you’re about to take. If you’re struggling with side effects, check in with your health care provider before you stop taking the medication. There may be specific remedies that can make your symptoms more manageable. That may allow you to complete the full course and ensure that your infection is wiped out.

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