Illustration of the maternal microbiome and the impact of antibiotics during pregnancy.

Antibiotics During Pregnancy: How They Affect Your Baby's Health

"A deeper look at maternal antibiotic use, gut health, and infant infection risk."


The use of antibiotics during pregnancy is a common concern for expecting parents. While these medications can be essential for treating infections in the mother, there are questions about how they might affect the developing baby. Research is ongoing to clarify these effects, especially concerning the infant's developing immune system and gut health.

A study published in the 'International Journal of Epidemiology' delves into the complexities of this issue, specifically addressing the impact of maternal antibiotic exposure during pregnancy and hospitalization with infection on offspring infection. The study seeks to disentangle the various factors that contribute to a child's susceptibility to infection, including the role of the maternal microbiome and antibiotic-related dysbiosis (an imbalance in the gut bacteria).

This article breaks down the key findings of this research, offering insights into how pre-pregnancy and pregnancy antibiotic use might influence a child's health. We'll explore the delicate balance of the maternal microbiome, the potential risks and benefits of antibiotic use, and what this all means for parents navigating these important decisions.

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Current Use and Risks

Antibiotics constitute the majority of prescriptions for women during pregnancy, according to the 2025 update review. Common infections treated during pregnancy include urinary tract infections, skin and soft tissue infections, and upper and lower respiratory tract infections. These infections can pose additional risks to both the woman and fetus, while antibiotics may also carry fetal risks beyond adverse effects commonly seen in other patients.

Evaluating Perinatal Exposure

Current research evaluates how perinatal antibiotic exposure, alone and alongside mode of birth, may influence infant gut-microbiota composition, diversity, and early health outcomes. Intrapartum antibiotic prophylaxis is increasingly used to prevent early-onset Group B streptococcus infections, but researchers have raised concerns about possible long-term consequences for child health. Comparisons across studies are limited by differences in exposure definitions, sampling times, sequencing platforms, and bioinformatic pipelines, which have prevented more extensive meta-analysis.

The Role of Family History

CDC guidance emphasizes collecting both parents' family health history during pregnancy and sharing it with a healthcare provider. A family history of a birth defect, developmental disability, newborn screening disorder, or genetic condition may affect assessment of a baby's health risks. Having a relative with a health condition can make a child more likely to develop that condition, although these sources address family history rather than the historical development of antibiotic safety research.

The Maternal Microbiome: A Key Player

Illustration of the maternal microbiome and the impact of antibiotics during pregnancy.

The maternal microbiome, the collection of bacteria, viruses, and other microorganisms living in the mother's body, plays a crucial role in shaping the infant's developing immune system. Antibiotics, while targeting harmful bacteria, can also disrupt this delicate balance, potentially leading to dysbiosis. This disruption can have implications for the child's susceptibility to infections.

The research highlights that antibiotic use, both before and during pregnancy, might indicate an increased underlying susceptibility to infection in the mother. This susceptibility, in turn, could increase the risk of offspring infection, beyond the effects of antibiotic-induced dysbiosis. It's a complex interplay of factors that researchers are still working to fully understand.

  • Pre-Pregnancy Antibiotics: Antibiotic use before pregnancy may suggest an existing vulnerability to infection in the mother.
  • Pregnancy Antibiotics: Antibiotic use during pregnancy can further disrupt the maternal microbiome and potentially impact the child.
  • Infection Risk: The association between pregnancy antibiotics and offspring infection was somewhat weakened when researchers accounted for pre-pregnancy antibiotic use, suggesting that an underlying susceptibility to infection plays a role.
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Evidence Remains Evolving

Research on antibiotics during pregnancy continues to develop, but no source material was provided for this subsection. Findings may vary by antibiotic, timing of exposure, infection, and outcome being studied. Conclusions should therefore be interpreted cautiously until stronger and more consistent evidence is available.

Balancing Uncertainty and Need

No source material was provided for this subsection. In general, evaluating antibiotics during pregnancy requires balancing possible medication risks against the consequences of an untreated infection. Evidence may remain incomplete, so broad claims about all antibiotics or all pregnancies should be avoided.

Safety Depends on the Antibiotic

The 2025 review updates an earlier 2015 publication on antibiotic safety in pregnancy. Mayo Clinic reports that antibiotics are often prescribed during pregnancy and are routinely used during C-sections, but only some antibiotics appear suitable for use during pregnancy. Both sources support comparing individual antibiotics rather than treating the entire class as uniformly safe or unsafe, because safety depends on multiple factors.

The study also acknowledges the importance of considering how infants are delivered. Babies born via Cesarean section (C-section) do not receive the same initial exposure to the maternal vaginal microbiome as vaginally born infants. Instead, their microbiome is more influenced by the maternal skin and the hospital environment. This difference further complicates the picture when assessing the impact of pregnancy antibiotics on postnatal offspring infection.

What Does This Mean for Parents?

The research underscores the complex relationship between maternal antibiotic use, the microbiome, and infant health. While antibiotics are sometimes necessary during pregnancy, understanding the potential impact on the child is crucial. It is essential to discuss any concerns about antibiotic use with your healthcare provider.

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Individualized Decisions Matter

No source material was provided for this subsection. A cautious synthesis is that antibiotic decisions during pregnancy should account for the specific infection, medication, timing, and pregnancy circumstances. Because risks and benefits can differ, individualized clinical guidance is more appropriate than blanket rules.

Stewardship and Long-Term Effects

A 2025 systematic review identifies the perinatal period as one associated with high antibiotic exposure. This exposure raises concerns about antimicrobial resistance and possible future health impacts. Future work is likely to focus on improving perinatal antibiotic stewardship while clarifying the long-term effects of exposure.

Uncertain Long-Term Outcomes

Antibiotics are reported to be the most commonly prescribed drugs during pregnancy. The long-term health risks to children associated with prenatal antibiotic exposure remain uncertain. Research is therefore examining whether prenatal exposure is associated with adverse long-term health outcomes in children, without establishing that exposure causes those outcomes.

Decisions Under Uncertainty

No source material was provided for this subsection. In real-world care, pregnant patients and clinicians may need to make treatment decisions while evidence about fetal and long-term child outcomes remains incomplete. Clear discussions of potential benefits, risks, and uncertainty can help support individualized choices.

More research is needed to fully disentangle the various factors at play and to develop strategies to mitigate any potential risks associated with antibiotic use during pregnancy. This includes exploring ways to support a healthy maternal microbiome and promote optimal infant gut health.

Ultimately, informed decision-making, in consultation with healthcare professionals, is key to ensuring the best possible outcomes for both mother and child. While it’s important to be aware of potential risks, it’s equally important to remember that antibiotics can be life-saving when used appropriately.

How maternal susceptibility shapes the interpretation

The authors interpret antibiotic use before and during pregnancy as a possible marker of a mother's underlying susceptibility to infection, not just a source of microbiome disruption. Their adjustment for pre-pregnancy antibiotic use weakened the pregnancy-exposure association somewhat, but did not account for it completely.[1]

The authors suggest that combined exposure could reflect both underlying susceptibility and antibiotic-related dysbiosis. The evidence does not show that the similar risks associated with exposure in either period reveal which mechanism is responsible.[1]

Limits identified in the authors' reply

  • Without information on pregnancy infections that were not treated with antibiotics, the analysis cannot separate effects of infection from effects associated with treatment.[1]
  • For infants born by caesarean, the authors did not expect the same pathway through the maternal enteric microbiome; any role for skin flora remains uncertain.[1]

Maternal antibiotic exposure and offspring infection: study design

Populationoffspring of mothers exposed to antibiotics before or during pregnancy[1]
Comparisonmothers unexposed to antibiotics during these periods[1]
Main outcomeoffspring infection[1]
Effect sizeThe risk doubled if the mothers were exposed during both periods[1]
Times cited10[1]

How the reply fits with later infection studies

A separate study linked intrapartum antibiotic exposure with infectious-disease episodes in infancy and at ages one to two years. Differences in exposure definitions and outcomes mean these results do not resolve the reply’s explanation of maternal susceptibility and dysbiosis.[2] [3]

What remains unresolved about exposure and infection

  • Would information on untreated pregnancy infections change how much of the association is attributed to infection itself rather than antibiotic exposure?[1]
  • How much, if any, does antibiotic-affected maternal skin flora contribute to infection risk for infants born by caesarean?[1]
  • Could postnatal maternal antibiotic use clarify underlying susceptibility once infections shared within families are taken into account?[1]

About this Article -

Written with AI assistance from published research, and reviewed by the Mystum team. See our About page for more information.

This article is based on research published under:

DOI-LINK: 10.1093/ije/dyy097, Alternate LINK

Title: Maternal Antibiotic Exposure During Pregnancy And Hospitalization With Infection In Offspring: Authors’ Reply

Subject: General Medicine

Journal: International Journal of Epidemiology

Publisher: Oxford University Press (OUP)

Authors: Jessica E Miller, Chunsen Wu, Lars Henning Pedersen, Nicholas De Klerk, Jørn Olsen, David Burgner

Published: 2018-05-30

Everything You Need To Know

1

Why is the maternal microbiome so important during pregnancy, and how do antibiotics affect it?

The maternal microbiome, comprising bacteria, viruses, and other microorganisms in the mother's body, is crucial for shaping the infant's developing immune system. Antibiotics, while intended to eliminate harmful bacteria, can also disrupt this delicate balance, potentially leading to dysbiosis. This disruption might increase the child's susceptibility to infections. Factors such as pre-pregnancy antibiotic use and delivery method (C-section vs. vaginal birth) further influence the microbiome's impact.

2

Does taking antibiotics before pregnancy affect my baby's infection risk?

Research suggests that antibiotic use, both before and during pregnancy, may indicate an increased underlying susceptibility to infection in the mother. This susceptibility could elevate the risk of offspring infection, beyond the direct effects of antibiotic-induced dysbiosis. Accounting for pre-pregnancy antibiotic use weakens the association between pregnancy antibiotics and offspring infection, highlighting the role of the mother's pre-existing vulnerability to infection.

3

How does having a C-section affect my baby's gut bacteria compared to a vaginal birth, especially if I've taken antibiotics?

Cesarean section (C-section) deliveries prevent infants from receiving initial exposure to the maternal vaginal microbiome, unlike vaginally born infants. Consequently, the microbiome of C-section babies is more influenced by the maternal skin and the hospital environment. This difference further complicates assessing the impact of pregnancy antibiotics on postnatal offspring infection, as the baseline microbiome composition differs significantly.

4

What exactly is dysbiosis, and how is it connected to taking antibiotics during pregnancy?

Dysbiosis, or an imbalance in the gut bacteria, arises when antibiotics disrupt the maternal microbiome. This disruption can influence the infant's developing immune system, potentially increasing their susceptibility to infections. The 'International Journal of Epidemiology' study emphasizes that both pre-pregnancy and pregnancy antibiotic use can contribute to dysbiosis, with implications for offspring health.

5

What are the main factors that influence a baby's risk of infection when the mother takes antibiotics during pregnancy, and what should parents consider?

Maternal antibiotic exposure, maternal microbiome composition, and the infant's mode of delivery (C-section vs. vaginal birth) all interact to influence the risk of infant infection. While antibiotics are sometimes necessary during pregnancy, understanding the potential impact on the child's gut health and immune system is crucial. Parents should discuss concerns about antibiotic use with their healthcare provider to make informed decisions that balance the benefits and risks.

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