The Vaginal Microbiome: An Overlooked Factor in Antibiotic Resistance

Antibiotic resistance

Your vaginal microbiota is home to a wide variety of microorganisms that contribute to vaginal health. But did you know that it can also contain genes that confer resistance to antibiotics?

About this article

Created 09 November 2026

Updated 13 November 2026

Antibiotics are used to treat bacterial infections and have saved millions of lives, including those of pregnant women. But their use, especially when excessive or inappropriate, promotes the selection of resistant bacteria: susceptible bacteria are eliminated, while resistant ones survive, multiply, and become difficult to treat. So much so that bacterial antibiotic resistance has become a major public health issue recognized by the World Health Organization (WHO).

19 Maternal-fetal infections are a major complication of pregnancy, accounting for approximately 19 million cases worldwide in 2021.²

13,4 An estimated 13.4 million babies were born preterm in 2020 (before 37 completed weeks of gestation).²

4,7 Bacterial antimicrobial resistance was estimated to be associated with more than 4.7 million deaths globally in 2021.³

The vaginal microbiota: an overlooked reservoir of antibiotic resistance?

Since these resistances can be transmitted from one bacterium to another through gene exchange, scientists are tracking their presence not only in our environment but also in our bodies, as they can hide in our microbiota. While resistance within the gut, oral, and skin microbiota has already been studied, their presence within the vaginal microbiota remained terra incognita, a field into which a French team (Institut Pasteur, Assistance Publique–Hôpitaux de Paris, Université Paris Cité) ventured. And sure enough: in 56% of the samples collected from the 1,547 pregnant women who participated in the study,¹ the researchers detected at least one gene associated with antibiotic resistance.

The vaginal microbiota, a reservoir of antibiotic resistance genes

https://www.biocodexmicrobiotainstitute.com/en/pro/vaginal-microbiota-reservoir…

The composition of the microbiota plays a role

Even more interesting: the bacterial composition of women's vaginal microbiota plays a role. Vaginal microbiota dominated by Lactobacillus crispatus had fewer resistance genes. Conversely, microbiota dominated by Lactobacillus iners or those that were more diverse and low in Lactobacillus exhibited greater diversity in resistance genes and a higher prevalence of mobile genetic elements, which can facilitate the transfer of resistance between bacteria. Researchers classify these communities into different CSTs (types of bacterial communities). CST IV, which has low levels of lactobacilli, is frequently associated with vaginosis, though it is not necessarily pathological. The simultaneous presence of certain bacteria, antibiotic resistance genes, and mobile genetic elements could promote their circulation within the vaginal microbiota, although such transfers were not demonstrated in this study. These findings highlight the importance of studying these communities to better understand vaginal health.

Researchers identify five major types of vaginal communities,⁴ known as CSTs (Community State Types), based on the bacteria that they contain.

3 optimal types in terms of vaginal health, dominated by lactobacilli: CST I, dominated by Lactobacillus crispatus; CST II, dominated by L. gasseri; and CST V, dominated by L. jensenii;
1 suboptimal type, CST III, dominated by another Lactobacillus (L. iners), which is much more susceptible to dysbiosis;
and 1 suboptimal type characterized by its low Lactobacillus content (type IV).

A concern for pregnancy?

Researchers have also observed links between certain vaginal microbiota profiles, antibiotic resistance genes, and pregnancy complications. Women who experienced preterm labor or preterm premature rupture of membranes were more likely to exhibit certain changes in the vaginal microbiota, including an increase in bacteria such as E. coli and K. pneumoniae and a decrease in several lactobacilli. These profiles were also associated with changes in antibiotic resistance genes, particularly those associated with β-lactam resistance, in cases of preterm premature rupture of membranes.

And all of this could affect the outcome of the pregnancy: women who experienced complications during childbirth (preterm labor or preterm delivery) had a diverse vaginal microbiota (increased levels of E. coli and K. pneumoniae, a decrease in several species of Lactobacillus) and more genes conferring resistance to β-lactams.

While these results represent a step forward, they must be interpreted with caution: detecting a resistance gene does not mean it is active; the presence of mobile genetic elements suggests exchanges, but the study does not prove that these transfers actually took place; and so on. Further studies will be needed to understand whether these resistances can be transmitted—particularly from mother to newborn—and what their potential health consequences might be. So researchers still have their work cut out for them.

Sources

_{1. Boutouchent N, Baud A, Tazi A et al. Bacterial community structure shapes the vaginal resistome during pregnancy. npj Biofilms Microbiomes (2026). https://doi.org/10.1038/s41522-026-01144-y.}

_{2. https://www.who.int/fr/news-room/fact-sheets/detail/preterm-birth.}

_{3. https://www.who.int/news-room/fact-sheets/detail/antimicrobial-resistance.}

_{4. What is vaginal microbiota, what is it made of?.}