March 24, 2023

Antibiotics for infection in little ones: what you need to know


  • Babies and toddlers are often prescribed antibiotics for infection. While it may be tempting to reach for antibiotics when your little one isn’t feeling well, it’s important to know that these medications only work against bacteria, not viruses.
  • Ask your provider what is causing your baby’s illness and if possible, stay away from antibiotics for viral infections. There are alternative ways to make your little one feel better in such cases.
  • Antibiotics may disrupt the gut microbiome, but there are ways you can help restore its balance to prevent possible antibiotic side effects and long-term health complications.

When used correctly, antibiotics help control infections, thus preventing serious health consequences. However, they are not the answer for every type of infection, and using them when not appropriate can do more harm than good.

Antibiotics only work against bacterial infections, not viral ones.

We get it, as a parent, you want to take good care of your little one, especially when it comes to illness. That’s why we put together this article on common infections in little ones, which ones can be safely managed in an alternative way to prevent the overuse of antibiotics, and how to reverse side effects of antibiotics.

Common infections in babies and toddlers

It may surprise you that many infections in little ones are actually caused by viruses.

While you always want to discuss the best treatment with your provider, here are some of the most common infections in babies and toddlers and their recommended treatment [1]:

  • Ear infection (also called otitis media): Did you know that most ear infections are cured without the need for antibiotics? Depending on your little one’s age and the severity and length of the symptoms, ask your pediatrician to consider "watchful waiting". The immune system may be able to clear the infection on its own.
  • Respiratory Syncytial Virus (RSV): Around one third of babies under one year of age will have RSV infection, one of the main causes of bronchiolitis. Although most babies with RSV are treated at home, RSV infection is the number one cause of hospitalization for babies [2]. Antibiotics are not effective against viruses and treating bronchiolitis with antibiotics doesn’t provide important benefits for the baby [3].
  • Rhinitis: “Rhinitis” means runny nose.  It is usually viral or due to allergy. Rhinitis may need antibiotics if symptoms persist for more than 10-14 days without improvement or if it leads to an internal infection like sinusitis.
  • Sore throat, or pharyngitis: Most are caused by viruses, unless it is caused by group A Streptococcus bacteria, which can be diagnosed with a laboratory test. If bacterial, it’s usually treated with penicillins.
  • Colds: These are always caused by viruses, and so there is no need for antibiotics. 
  • Bronchitis:  Bronchitis causes a deep cough, which is, like colds, almost always caused by a virus and typically does not need to be treated with antibiotics. Your pediatrician can help distinguish between bronchitis and deeper lung infections like pneumonia.

Which ones could use antibiotics?

Antibiotics might be needed if bronchitis, bronchiolitis, or RSV infection progresses to bacterial pneumonia. Your pediatrician can help decide if further testing like an examination, an x-ray, lab tests, or an aspirate from the back of the throat are needed to determine if a bacterial infection is also present and if antibiotics should be used.

Antibiotics side effects: gut health and beyond

Antibiotics attack both good and bad bacteria. So when your little one takes an antibiotic, it not only gets rid of the bacteria responsible for the infection, it also impacts other bacteria normally present in the gut.

This unintended elimination of beneficial bacteria can favor the growth of unfriendly bugs, like those that produce diarrhea.

Studies show that after taking antibiotics, Proteobacteria levels usually rise [4]–[11]. Escherichia coli are Proteobacteria that normally live in the gut at low levels. The problem is that certain E. coli strains can proliferate and can cause diarrhea and other serious illnesses. 

Clostridioides difficile is another species that may survive antibiotic treatment and cause severe diarrhea. 

What about the long term side effects of antibiotics? Antibiotics can make babies more prone to suffer from an allergic disease, such as eczema and asthma [12]–[19]. For example, cephalosporins might make your baby 1.4 to 2.4 times more likely to develop an allergy to cow’s milk [20], [21].

Protecting the microbiome: antibiotics are not always necessary

In the US, around 22% of babies and 29% of toddlers who visit the emergency department are prescribed antibiotics. A concerning issue is that in about 26% of cases, these prescriptions are unnecessary [22].

If they only work for bacterial infections, why do some providers prescribe antibiotics for viral infections? These are some of the reasons:

  • A respiratory viral infection might end up as a bacterial infection if not treated appropriately, so many providers feel that it is safer to prescribe antibiotics just in case [23], [24].
  • Many parents feel better if their little one is prescribed something and may demand unnecessary antibiotics. Instead of explaining why antibiotics won’t work, providers prescribe them to fulfill the parents’ expectation [24]–[26].
  • Providers might not know that the overuse of antibiotics contributes to the spread of antibiotic resistance among bacteria [24]. Multi-drug resistant bacteria, also known as superbugs, are a worldwide concern and extremely difficult to manage.
  • Providers might not realize the enormous impact antibiotics can have on the gut microbiome and how much that can affect your baby’s overall health [27].

Now that we’ve got you concerned: What can you do?  

If possible, work with your provider to determine if an antibiotic is the most effective treatment. Ask them whether your baby or toddler has a viral or bacterial infection.

If the infection is viral, you may want to turn to alternative treatments to relieve pain and discomfort. Some suggestions you can try:

  • For ear infection, apply gentle heat and massage the area around the ear. This may help drain fluids and relieve pain 
  • Cool-mist humidifiers or a steamy bathroom may help with viral bronchitis or bronchiolitis.
  • Nasal saline drops or suctioning may help with nasal congestion.
  • Eucalyptus honey is a natural option to relieve cough that can be given to toddlers (older than one year of age) [28].
  • A sponge bath with lukewarm water may help reduce fever.

Ask your provider about possible complications to watch out for (symptom duration, persistent high fever, problems breathing, etc.) that may require a second evaluation.

When antibiotics are actually needed

If bacterial infection is confirmed or highly suspected, consider asking your provider if a test to check for antibiotic susceptibility would be helpful for choosing a specific antibiotic that does the least damage to beneficial gut microbes. This is rarely an option in respiratory infections, but might be possible for infections in the gut, urine, or blood.

When such a test is not an option, your provider will likely prescribe what is most appropriate based on previous treatments and local infection patterns.

Stay informed, ask which class of antibiotics your baby is being prescribed. A narrow-spectrum antibiotic (such as amoxicillin) is better than a broad-spectrum antibiotic (such as amoxicillin/clavulanate) as it will have less impact on the gut microbiome and will lead to less resistant bacteria.

Be sure to give your little one the full antibiotic treatment, with the appropriate dose at the appropriate time, even if symptoms improve before the end of the treatment. This will efficiently end the infection and will help prevent the emergence of resistant bacteria.

How to reverse side effects of antibiotics on the gut microbiome

Sometimes antibiotics are absolutely necessary. If your baby has taken antibiotics, don’t worry because there are a number of things you can do to increase the amount of  beneficial bacteria and restore the balance of your baby’s microbiome:

  • Probiotics. Using probiotics during and after antibiotic treatment can prevent antibiotic side effects. We recommend giving your little one probiotics as soon as they start on antibiotics and continue for 1-2 additional weeks.
  • Breastmilk. If available, breastfeeding can counteract the antibiotics' effects on your baby’s microbiome. Breastmilk is loaded with nutrients and sugars that support the growth of beneficial Bifidobacterium. It also provides antibodies that will help prevent unfriendly bacteria from going wild [29].  
  • Food choices. If your little one is eating solids, choose low-fiber foods that will not irritate the gut while on antibiotics and a few days after. These include bananas, white rice, apple sauce, carrots, boiled potatoes, and bread toasts. Avoid grapefruit, as this fruit has some compounds that may interfere with proper antibiotic absorption [30]. Reincorporate high-fiber foods gradually to promote the growth of beneficial gut bacteria.
  • Lifestyle. Having pets, going outdoors, visiting farms, and choosing the right infant daycare can all help your baby’s gut microbiome return to normal after antibiotics.

It may also be worth considering a gut microbiome test to see what’s happening inside your baby’s gut. A comprehensive view of the gut microbiome can identify any areas of concern and guide you through a personalized roadmap to help restore your baby’s gut health.


[1] “Pediatric Outpatient Treatment Recommendations | Antibiotic Use | CDC,” May 03, 2021. (accessed Oct. 29, 2021).

[2] E. Thomas, J.-M. Mattila, P. Lehtinen, T. Vuorinen, M. Waris, and T. Heikkinen, “Burden of Respiratory Syncytial Virus Infection During the First Year of Life,” J. Infect. Dis., vol. 223, no. 5, pp. 811–817, Mar. 2021, doi: 10.1093/infdis/jiaa754.

[3] R. Farley, G. K. P. Spurling, L. Eriksson, and C. B. Del Mar, “Antibiotics for bronchiolitis in children under two years of age,” Cochrane Database Syst. Rev., no. 10, p. CD005189, Oct. 2014, doi: 10.1002/14651858.CD005189.pub4.

[4] N. A. Bokulich et al., “Antibiotics, birth mode, and diet shape microbiome maturation during early life,” Sci. Transl. Med., vol. 8, no. 343, p. 343ra82, Jun. 2016, doi: 10.1126/scitranslmed.aad7121.

[5] O. Brunser, M. Gotteland, S. Cruchet, G. Figueroa, D. Garrido, and P. Steenhout, “Effect of a milk formula with prebiotics on the intestinal microbiota of infants after an antibiotic treatment,” Pediatr. Res., vol. 59, no. 3, pp. 451–456, Mar. 2006, doi: 10.1203/01.pdr.0000198773.40937.61.

[6] F. Fouhy et al., “High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin,” Antimicrob. Agents Chemother., vol. 56, no. 11, pp. 5811–5820, Nov. 2012, doi: 10.1128/AAC.00789-12.

[7] K. Korpela et al., “Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children,” Nat. Commun., vol. 7, p. 10410, Jan. 2016, doi: 10.1038/ncomms10410.

[8] J. Penders et al., “Factors influencing the composition of the intestinal microbiota in early infancy,” Pediatrics, vol. 118, no. 2, pp. 511–521, Aug. 2006, doi: 10.1542/peds.2005-2824.

[9] E. P. K. Parker et al., “Changes in the intestinal microbiota following the administration of azithromycin in a randomised placebo-controlled trial among infants in south India,” Sci. Rep., vol. 7, no. 1, p. 9168, Aug. 2017, doi: 10.1038/s41598-017-06862-0.

[10] W. Morello et al., “Low-Dose Antibiotic Prophylaxis Induces Rapid Modifications of the Gut Microbiota in Infants With Vesicoureteral Reflux,” Front. Pediatr., vol. 9, p. 674716, 2021, doi: 10.3389/fped.2021.674716.

[11] E. Van Daele et al., “Effect of antibiotics in the first week of life on faecal microbiota development,” Arch. Dis. Child. Fetal Neonatal Ed., vol. 107, no. 6, pp. 603–610, May 2022, doi: 10.1136/archdischild-2021-322861.

[12] Z. Aversa et al., “Association of Infant Antibiotic Exposure With Childhood Health Outcomes,” Mayo Clin. Proc., vol. 96, no. 1, pp. 66–77, Jan. 2021, doi: 10.1016/j.mayocp.2020.07.019.

[13] D. H. Kim, K. Han, and S. W. Kim, “Effects of Antibiotics on the Development of Asthma and Other Allergic Diseases in Children and Adolescents,” Allergy Asthma Immunol. Res., vol. 10, no. 5, pp. 457–465, Sep. 2018, doi: 10.4168/aair.2018.10.5.457.

[14] S. E. Zven, A. Susi, E. Mitre, and C. M. Nylund, “Association Between Use of Multiple Classes of Antibiotic in Infancy and Allergic Disease in Childhood,” JAMA Pediatr., vol. 174, no. 2, pp. 199–200, Feb. 2020, doi: 10.1001/jamapediatrics.2019.4794.

[15] Z. Zou, W. Liu, C. Huang, C. Sun, and J. Zhang, “First-Year Antibiotics Exposure in Relation to Childhood Asthma, Allergies, and Airway Illnesses,” Int. J. Environ. Res. Public. Health, vol. 17, no. 16, p. E5700, Aug. 2020, doi: 10.3390/ijerph17165700.

[16] K. Yamamoto-Hanada, L. Yang, M. Narita, H. Saito, and Y. Ohya, “Influence of antibiotic use in early childhood on asthma and allergic diseases at age 5,” Ann. Allergy Asthma Immunol. Off. Publ. Am. Coll. Allergy Asthma Immunol., vol. 119, no. 1, pp. 54–58, Jul. 2017, doi: 10.1016/j.anai.2017.05.013.

[17] S. Foliaki et al., “Antibiotic use in infancy and symptoms of asthma, rhinoconjunctivitis, and eczema in children 6 and 7 years old: International Study of Asthma and Allergies in Childhood Phase III,” J. Allergy Clin. Immunol., vol. 124, no. 5, pp. 982–989, Nov. 2009, doi: 10.1016/j.jaci.2009.08.017.

[18] D. M. Patrick et al., “Decreasing antibiotic use, the gut microbiota, and asthma incidence in children: evidence from population-based and prospective cohort studies,” Lancet Respir. Med., vol. 8, no. 11, pp. 1094–1105, Nov. 2020, doi: 10.1016/S2213-2600(20)30052-7.

[19] F. Kelderer, I. Mogren, C. Eriksson, S.-A. Silfverdal, M. Domellöf, and C. E. West, “Associations between pre- and postnatal antibiotic exposures and early allergic outcomes: A population-based birth cohort study,” Pediatr. Allergy Immunol. Off. Publ. Eur. Soc. Pediatr. Allergy Immunol., vol. 33, no. 9, p. e13848, Sep. 2022, doi: 10.1111/pai.13848.

[20] J. Metsälä, A. Lundqvist, L. J. Virta, M. Kaila, M. Gissler, and S. M. Virtanen, “Mother’s and offspring’s use of antibiotics and infant allergy to cow’s milk,” Epidemiol. Camb. Mass, vol. 24, no. 2, pp. 303–309, Mar. 2013, doi: 10.1097/EDE.0b013e31827f520f.

[21] A. G. Hirsch et al., “Early-life antibiotic use and subsequent diagnosis of food allergy and allergic diseases,” Clin. Exp. Allergy J. Br. Soc. Allergy Clin. Immunol., vol. 47, no. 2, pp. 236–244, Feb. 2017, doi: 10.1111/cea.12807.

[22] N. M. Poole, D. J. Shapiro, K. E. Fleming-Dutra, L. A. Hicks, A. L. Hersh, and M. P. Kronman, “Antibiotic Prescribing for Children in United States Emergency Departments: 2009-2014,” Pediatrics, vol. 143, no. 2, p. e20181056, Feb. 2019, doi: 10.1542/peds.2018-1056.

[23] H. J. Cho, S. J. Hong, and S. Park, “Knowledge and beliefs of primary care physicians, pharmacists, and parents on antibiotic use for the pediatric common cold,” Soc. Sci. Med. 1982, vol. 58, no. 3, pp. 623–629, Feb. 2004, doi: 10.1016/s0277-9536(03)00231-4.

[24] R. S. Md Rezal, M. A. Hassali, A. A. Alrasheedy, F. Saleem, F. A. Md Yusof, and B. Godman, “Physicians’ knowledge, perceptions and behaviour towards antibiotic prescribing: a systematic review of the literature,” Expert Rev. Anti Infect. Ther., vol. 13, no. 5, pp. 665–680, May 2015, doi: 10.1586/14787210.2015.1025057.

[25] J. Strumiło, S. Chlabicz, B. Pytel-Krolczuk, L. Marcinowicz, D. Rogowska-Szadkowska, and A. J. Milewska, “Combined assessment of clinical and patient factors on doctors’ decisions to prescribe antibiotics,” BMC Fam. Pract., vol. 17, p. 63, Jun. 2016, doi: 10.1186/s12875-016-0463-6.

[26] P. P. Dempsey, A. C. Businger, L. E. Whaley, J. J. Gagne, and J. A. Linder, “Primary care clinicians’ perceptions about antibiotic prescribing for acute bronchitis: a qualitative study,” BMC Fam. Pract., vol. 15, p. 194, Dec. 2014, doi: 10.1186/s12875-014-0194-5.

[27] M. Wilson, M. J. Mello, and P. A. Gruppuso, “Antibiotics and the Human Microbiome: A Survey of Prescribing Clinicians’ Knowledge and Opinions Regarding the Link between Antibiotic-Induced Dysbiosis and Immune-Mediated Disease,” R. I. Med. J. 2013, vol. 104, no. 7, pp. 59–63, Sep. 2021.

[28] H. A. Cohen et al., “Effect of honey on nocturnal cough and sleep quality: a double-blind, randomized, placebo-controlled study,” Pediatrics, vol. 130, no. 3, pp. 465–471, Sep. 2012, doi: 10.1542/peds.2011-3075.

[29] O. Ballard and A. L. Morrow, “Human milk composition: nutrients and bioactive factors,” Pediatr. Clin. North Am., vol. 60, no. 1, pp. 49–74, Feb. 2013, doi: 10.1016/j.pcl.2012.10.002.

[30] D. Genser, “Food and drug interaction: consequences for the nutrition/health status,” Ann. Nutr. Metab., vol. 52 Suppl 1, pp. 29–32, 2008, doi: 10.1159/000115345.