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Why You Should Think Twice before Giving Your Child Antibiotics


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Antibiotics are necessary and can even save lives, but they are also overprescribed and misused. When antibiotics are prescribed to children for viral (rather than bacterial) illnesses, they are ineffective and can cause lifelong changes to gut bacteria, metabolism, and the immune system. Read on to find out when antibiotics are appropriate, and learn strategies to reduce the need for antibiotics and to protect your children’s microbiome and future health.

antibiotics for kids
Antibiotics for kids are sometimes necessary, but are often over used. istock.com/Kontrec

Antibiotics are among the most frequently prescribed medications for children. One out of every five pediatric acute-care visits resulted in an antibiotic prescription (1). By age 20, the average American child has received 17 courses of antibiotics (2).

Unfortunately, overuse of antibiotics starts even earlier. In the U.S., about 40 percent of women get antibiotics during delivery, just as their babies are acquiring their crucial microbes. To top that off, most American-born babies are given an antibiotic immediately following birth. This was a historical practice designed to protect a newborn from eye infections if the mother had gonorrhea, but it is now regular practice, regardless of the mother’s STD status (3).

The worldwide rise in antibiotic resistance has alarmed the medical community. Pathogenic bacteria are becoming resistant to antibiotics. (4) Potentially dangerous bacteria that are immune to antibiotics could become “super bugs” that have no cure.

Fortunately, some doctors have cut back on their use of antibiotics and now prescribe them only when strictly necessary. However, as a parent, you still need to be watchful when antibiotics are prescribed to your children.

Many Childhood Illnesses Do Not Benefit from Antibiotics: Colds, Ear Infections, and Sore Throats

Antibiotics kill bacteria, not viruses. Nonetheless, many doctors prescribe antibiotics for childhood illnesses that are viral, meaning that antibiotics are unlikely to have any effect.

The two most common reasons for pediatric antibiotic prescriptions are upper respiratory infections and ear infections, of which 60 to 73 percent are estimated to be viral (5). Most childhood sore throats are caused by viruses too. Let’s take a look at each of these separately.

Upper respiratory infections (URIs) such as the common cold or the flu are mainly caused by viruses. As many as 80 percent of URIs are viral in nature and can be traced to microbes such as rhinovirus, parainfluenza, and metaphenumovirus (6). Antibiotics target bacteria only and have no effect on the outcome of viral infections. One study showed that antibiotics were prescribed about 57 percent of the time for acute respiratory tract infections despite the fact that only 27 percent were bacterial. Extrapolation of this data leads to an estimate that there are up to 11.4 million unnecessary prescriptions for antibiotics every year! (5)

Ear “infections” don’t necessarily benefit from antibiotics either. A recent systematic review found that 24 hours after the start of treatment, 60 percent of children had recovered from their ear infections, whether or not they received an antibiotic. Children in the antibiotic group were also more likely to experience adverse events such as rash, vomiting, or diarrhea (7).

When are antibiotics appropriate for children?

When researchers compared immediate antibiotic treatment to a “wait and see” approach, there was no improvement in pain associated with ear infection at follow-up visits and no difference in ear abnormalities or symptom recurrence. This makes you question whether antibiotics help at all in these cases. Antibiotics were most useful in children under age 2 with bilateral ear infections and discharge. In most other cases, a wait-and-see approach was best (7).

In fact, the medical term for “ear infection” is otitis media, which literally means “middle ear inflammation.” It does not necessarily indicate an infection. Some cases may actually be caused by food allergies or food sensitivities, most commonly to dairy products (8). Ironically, treating these cases with antibiotics may alter gut bacteria and further increase food sensitivities.

Sore throats shouldn’t typically be treated with antibiotics, either. In children under 5 years old, 95 percent of sore throats are viral. In older children (ages 5 to 16), 70 percent of sore throats are viral. (9) In fact, only 20 percent of sore throats are thought to be caused by bacterial infection. (10) The bacteria that most commonly leads to sore throat is group A B-hemolytic streptococcus, but up to 30 percent of healthy people carry this bacteria without any problems. Most sore throats will clear up on their own and do not pose serious after effects. (9) Martin Blaser’s book, Missing Microbes, summarizes more of this research. (2)

Why We Shouldn’t Take Antibiotics so Lightly

Overusing and misusing antibiotics has long-term consequences for children’s health. When you take an antibiotic by mouth, it is absorbed in your gut and enters the bloodstream.

Once in circulation, it travels to all of your organs and tissues, destroying bacteria wherever it finds them.  Broad-spectrum antibiotics are especially adept killers, targeting a wide variety of bacteria, including many beneficial microbes. As you can see, oral antibiotics are not a very precise treatment. Regardless of where the infection might be, they affect the entire body and they take out a lot of innocent bystanders.

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Four long-term risks of childhood antibiotics


#1. Changes to the gut microbiota
Every day we are learning new things about the human microbiome, which outnumbers the cells in our bodies ten to one. Seventy percent of the immune system resides in the gut (11) and the microbiota collaborate with the immune system to protect and defend us.

Gut bacteria influence:

  • Immune function
  • Metabolism
  • Nutrition
  • Detoxification
  • Inflammation
  • Weight gain

A recent study (2016) showed that one single treatment with antibiotics leads to serious and long-term changes to the gut microbiota. In Finnish children, a single course of macrolide antibiotics caused major changes in the gut microbiota, and these changes were not reversed until nearly two years after the antibiotic course was completed. (12) Macrolide antibiotics include erythromycin, azithromycin, and clarithromycin.

The study showed that children who took antibiotics had:

  • Lower Actinobacteria, including Bifidobacterium, which is a beneficial gut bacteria commonly used in probiotics. (13)
  • Higher gram-negative phyla Bacteroidetes and Proteobacteria, which are thought to be opportunistic pathogens.
  • Lower bile-salt hydrolase (BSH), an enzyme that mediates host-microbe communication and has been shown to play a role in cholesterol metabolism and weight gain in mice. (14)
    Higher macrolide antibiotic resistance, meaning these antibiotics may not work later in life.

Not only that, but the diversity of the microbial communities didn’t return to normal until approximately two years after the antibiotic course. This means that most children’s gut flora do not have time to recover because two years is longer than the average time between courses of antibiotics (1.5 to 1.8 doses per year). (12)

For more on this topic, see my article on how antibiotics affect our gut flora.

The impact of antibiotics on gut bacteria might be directly or indirectly related to the higher rates of inflammatory bowel disease, asthma, allergies, and impaired metabolism that we see in children who are given higher levels of antibiotics.

#2. Gut inflammation
A study in Denmark showed that children who develop inflammatory bowel disease (IBD) are 84 percent more likely to have received antibiotics in their lifetime.  Children who had taken antibiotics were more than three times as likely to develop Crohn’s disease (CD) than those who had never taken antibiotics, and each individual course of antibiotics was associated with an 18 percent increased risk of CD. (15)

#3. Asthma, eczema, and allergies
Asthma was almost twice as likely to develop in children who had received antibiotics in the first year of life than those who had not. The risk was highest in children receiving more than four courses of antibiotics, and especially those receiving broad-spectrum antibiotics like cephalosporin. (16) Antibiotic use in the first year of life is also associated with rhinoconjunctivitis and eczema in children. (17)

Both antibiotic use during pregnancy and early-life antibiotic use have been associated with increased risk of food allergies. The risk of food allergy increases with the increasing number of antibiotic courses. (18, 19).

#4. Metabolism and weight
Antibiotics also have an impact on metabolic health and body weight. Early life antibiotic use increases a person’s risk of being overweight in later life. (12) Fecal microbiota composition in infancy can predict whether a child will be overweight or normal weight at age seven. (20) In animals, even a short-term disruption to the microbiota from antibiotics changed gene expression in the small intestine and led to lifelong changes in body composition. (21)

Thanks to the gut flora, early life appears to be an especially critical period of development for the metabolism and the immune system, during which time even short-term disruptions can have lasting effects. (22, 23)

Lower Your Child’s Antibiotic Prescriptions with These Five Simple Steps

The most important step you can take toward reducing antibiotic use in your children is preventing the need for them in the first place. Here are five key steps you can take to do that:

  1. Feed them a nutrient-dense, whole foods diet to reduce the likelihood, frequency, and severity of childhood infections.
  2. Have your children wash their hands frequently to reduce their exposure to infectious germs. A good habit to get into is washing hands just after they get home from school or other outings, in addition to the typical times (before meals, after using the bathroom, etc.).
  3. Give them supplemental nutrients that can prevent or shorten the duration of infections
  4. Encourage their consumption of fermented foods and fermentable fiber to support gut health, and consider supplemental probiotics and prebiotics.
  5. Consider botanical remedies that can shorten the duration of viral infections, improve immunity, and provide symptom relief.

If your doctor does prescribe antibiotics, ask if he or she is certain that the condition is bacterial in origin and whether the condition requires antibiotics or may safely resolve on its own without them. “Watching and waiting” is a valid strategy that is often preferable to treating with antibiotics prophylactically.

That said, there are times when antibiotics are necessary. If you and your doctor determine there is a good reason for your child to take them, there are things you can do to reduce the long-term effects. These include taking probiotics and prebiotics, consuming bone broth, and supporting healthy liver detoxification.

I hope this article has made it clear that antibiotics should be given only after careful consideration, especially if the condition your child has is likely to be viral. Antibiotics have a time and a place, but since they can have wide-ranging effects on the gut flora, metabolism, allergy, and inflammation, they should be used with discretion.

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Join the conversation

  1. Hi Chris,
    My 12 yr old son has had a major weight increase in the last 3 years (50+ lbs) which is definitely more than just a ‘growing’ boy. I know now (unfortunately) that the over prescribed antibiotics and immunizations throughout his childhood had an affect on his gut biome. What tests would you recommend to determine treatment and begin the healing process?

    Thank you in advance!

  2. my granddaughter is two and a half and has just been diagnosed with scarlet fever and yet the doctor has not prescribed her anti biotics, seeing that scarlet fever is caused by a bacteria, so we have to just sit it out. i am wondering why it hasnt been prescribed .i have read information online and the general treatment is anti biotics.perhaps the doctor thinks she is strong enough to battle the bacteria. but i do worry.

  3. On the contrary, if antibiotics are not prescribed and an infection is not found and treated the results can be much worse than a simple rash, or something that requires a bit of continuous monitoring throughout the child’s life. I say this because we were informed today that a simple, untreated bacterial infection was the cause of our sweet baby boy’s death 3 weeks ago, at the age of 5 months and 5 days. We had asked about antibiotics on multiple occasions due to prolonged symptoms, and had told the 4 doctors who saw our son that he was not getting better on his own. We were told to wait it out and keep an eye on him. They said we should use nasal saline, a bulb aspirator, a cool mist humidifier, baby Vicks and keep him from lying flat. We did all of those things, and repeatedly told the doctors he was not getting better. They refused antibiotics to our son, and he died. If you think your child needs an antibiotic, make it happen. Anything an antibiotic can cause is much better than losing your child.

    • I had to demand this from my child’s doctor. May daughter was sick for over a month demand a blood test. Daughter didn’t want to do it because of cost. After a month she did it. Daughter had ebstein Barr and mycoplasma pneumonia. Still was worried about giving antibiotics because she might get c diff. I told her she is going to have to worry about getting sued if she doesn’t treat my daughter. Daughter missed 20 days of school. On antibotics after day three was bouncing around like a rabbit!! Doctors are getting stupid about this!!

  4. My baby has had four rounds of antibiotics by 7 months. One for viral, one for skin infection, one for allergic reaction to keflex do the dr changed it another antibiotic for skin infection, and one for uti (hospital nurse gave it to my baby). She has severe eczema. How can we heal her? She is still only breastfed at 9 months?

  5. Perhaps someone can give us input. My granddaughter did in fact need and receive an antibiotic at birth. My daughter had strep when she delivered. Whether or not they baby should or shouldn’t have gotten an antibiotic is up to debate, but the fact is, is that she did. So now, we are dealing with the consequences in terms of reflux, gas etc. She is a month old now. She is on a probiotic, gripe water and other homeopathic remedies. Does anyone have any solid suggestions on how to improve her microbiome? My daughter is breastfeeding, and eating totally paleo.

  6. I am late to the conversation, but need some opinions regarding pediatric dental pain with fever. Antibiotics have been suggested until the tooth is further evaluated and treated (there is a cavity in the tooth). What alternatives are there to antibiotics for this situation?

    • Check out iodine for oral rinsing ( diluted) and supplementing- natures best antiviral and antibacterial!

  7. My son was diagnosed with Sickle cell @ birth. And was prescribed antibiotics for the first 5 years of his life to prevent bacterial infection, how do I go around this? I questioned his doctor and they claim it’s ok, as it’s not a high dose (50ml Amoxacilin) every 12hrs.

    • Good question! My daughter is slso taking penicillin twice daily for prophylactic treatment to prevent infection due to sickle cell disease.

  8. My son had a UTI at 10 days old caused by urine reflux from urinery tract issues. This caused damage to one of his kidneys and ever since he has been prescribed and taken 5ml of caphalexin daily and now he is four. I am worried this will have similar long term issues as per your article. Do I have cause for concern?

    • Have you considered surgery to fix his reflux? I had constant kidney infections as a child and eventually got a ureteral reimplantation surgery at age 6. This stopped my infections and I didn’t have to be on antibiotics anymore. My kidney was pretty severely damaged before they were able to do the surgery, but even still I have been infection-free for 20 years.

  9. I think many doctors do not make the distinction between bacterial and viral infections when prescribing antibiotics. This may be to get rid of the infection in the short term. I think they tend to treat the symptoms and not the root cause. No wonder my Dad refuses to let his doctor prescribe him any.
    A real eye-opener. Keep up the good work

  10. Hi from the UK,
    I listened with interest to your podcast hosted by Steve Wright on how to treat Reflux in babies.
    My little girl is now 8wks old, she was born naturally, but unfortunately the waters were broken from Sunday midday and she was delivered on the Tuesday just after 1pm, I had developed a slight temperature in labour – we were then both immediately given 48 hrs of intravenous antibiotics. Which I’m not sure was necessary, but unfortunately that was the pedeatrician’s very strong advice at the time. She has a lot of digestive issues. She is breast fed and a good weight. My GP (this may be a British thing – General Practioner), has prescribed her infant Gaviscon, which I give to her via oral syringe before each feed. Without this, feeding is pretty impossible as she is very fussy on the breast while feeding. She clearly suffers from digestive discomfort sometimes an hour, hour and a half after feeding. She brings back the milk and wind (she often gulps air during feeding or in between and gets hiccups a lot – she regularly hiccuped twice a day in the womb!) at various stages of digestion (sometimes fairly immediately when it’s still milky and sometimes much later when it is more like runny cottage cheese!). Having listened to your podcast I have bought her the Klaire Labs – Ther-Biotic Infant Formula. Because of the Gaviscon I’m unsure when best to give this to her as I wondered if it would impede absorption if given in conjunction with her feed?
    I would greatly appreciate your thoughts and advice. Many thanks in advance,

  11. Hi Chris,
    What about antibiotics use for a ruptured eardrum? My twelve month old son has an ear infection, we tried to wait and see, however his eardrum ruptured yesterday. The GP advices us to give antibiotics to prevent infection. Do you have any advice in case of ruptured eardrums?

  12. My son had chronic ear infection. Doc just kept putting him on antibiotics. He had puss come out of his ear! I stopped the antibiotics and put him on probiotics. It eventually cleared up. I’m think he potentially had a yeast infection.

  13. I had a horrific, severe and persistent acne breakout at age 23. I was put on high dose trimethoprim for 2 months to see if it could delay Accutane. It worked beautifully, but what has followed has been hell. Multiple, high methane SIBO infections, hospitalisations due to alkalosis caused by bowel impaction all the way up to my small bowel, constant – and i mean constant – pain all around my abdomen and back, absent periods, reflux, and endless examinations. Still working on a cure to get my intestinal motility back. NEVER take Trimethoprim.

    • Things I’ve tried, low fiber, high fiber (grain and dairy free of course), low fodmap, low fodmap SIBO (SCD+FODMAP), senna, dulcolax, picolax, every other oTC and prescription motility agent on the market, at extreme costs, colonics, thousands on probiotics, enzymes, ACV, massage, IF, eating every 4hrs, smaller meals, juice fast, etc etc.