Use of antibiotics during pregnancy and the risk of major congenital malformations

Clindamycin, doxycycline, quinolones, macrolides and phenoxymethylpenicillin in utero exposure were linked to major congenital malformations

image of Clindamycin drugs

2017 Study Abstract

Few studies have investigated the link between individual antibiotics and major congenital malformations (MCMs) including specific malformations owing to small sample size. We aimed – population based cohort study, British Pharmacological Society, 19 July 2017 – to quantify the association between exposure to gestational antibiotic and the risk of MCMs.

Using the Quebec pregnancy cohort (1998 -2008), we included a total of 139,938 liveborn singleton alive whose mothers were covered by the “Régie de l’assurance maladie du Québec” drug plan for at least 12 months before and during pregnancy. Antibiotics exposure was assessed in the first trimester and MCMs were identified within the first year of life.

After adjusting for potential confounders, clindamycin exposure was associated with an increased risk of MCMs (aOR 1.34, 95%CI, 1.02-1.77, 60 exposed cases), musculoskeletal system malformations (aOR 1.67, 95%CI, 1.12-2.48, 29 exposed cases) and ventricular/atrial septal defect (aOR 1.81, 95%CI, 1.04-3.16, 13 exposed cases).

Doxycycline exposure increased the risk of circulatory system malformation, cardiac malformations and ventricular/atrial septal defect (aOR 2.38, 95%CI ,1.21-4.67, 9 exposed cases; aOR 2.46, 95%CI, 1.21-4.99, 8 exposed cases; aOR 3.19, 95%CI, 1.57-6.48, 8 exposed cases, respectively). Additional associations were seen with quinolone (1 defect), moxifloxacin (1 defect), ofloxacin (1 defect), macrolide (1 defect), erythromycin (1 defect) and phenoxymethylpenicillin (1 defect). No link was observed with amoxicillin, cephalosporins and nitrofurantoin. Similar results were found when penicillins were used as the comparator group.


  • Clindamycin, doxycycline, quinolones, macrolides and phenoxymethylpenicillin in utero exposure were linked to organ specific malformations.
  • Amoxicillin, cephalosporins and nitrofurantoin were not associated with MCMs.

2 thoughts on “Use of antibiotics during pregnancy and the risk of major congenital malformations”

  1. When my youngest was born, she did not make it into my room with me. She wasn’t breathing well, bluish, not doing well. Next morning I woke up with 2 doctors in my room, both our pediatrician and my OB doctor. And they were discussing my little girl. She had Group B Strep at birth.
    This was confusing to my OB doctor as I had tested negative for such, nor did I have any of the things which made it more likely. My pediatrician said how he wished all mothers were given an antibiotic before giving birth, then they would never have babies so sick. But she tested negative. Those tests don’t help much with this was the pediatrician’s opinion and if all moms were given the antibiotic it would never happen.
    Question is where did she pick up the strep B? Me even though I tested negative? from the hospital?
    I don’t know if they use amoxicillin for this, but not a fan of giving antibiotics to everyone. Nor am I a fan of sick babies who could easily die. She probably would not have made it without her pediatrician putting her on antibiotics while waiting for the test results to come back. He said worst case Group B strep. If that came back negative he would take her back off them. It was positive. Lots of prayers, blessings, her spinal tap and tests a few days later were all negative, her color so much better, more responsive. She kept pulling out her IV, they had to tape a cup over it on the top of her head.
    Just saying sometimes there is a case for antibiotics for mothers, being careful which ones.
    This was 20 years back, hopefully they have made progress on this. When she went in for checkups her doctor would marvel that there wasn’t anything wrong with her.
    I also believe she her food sensitivities, digestive tract irritation, even as a small child is linked to her first days of live on antibiotics. Better if I had the antibiotics (if that is how she picked it up) in this specific case.

    1. Thank you very much Heidi for sharing your story, very glad it all went went at the end 🙂

      With all respect, you might have misunderstood the post study. It does not say all antibiotics are bad.
      The study targets 5 specific types : Clindamycin, doxycycline, quinolones, macrolides and phenoxymethylpenicillin AND talks about MCMs risks linked to use during pregnancy – not after giving birth…

      Thanks again

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