Is the vaginal microbiota a reservoir of resistance genes?

This is the flip side of the coin when it comes to antibiotics : while their use has saved many lives, it has also gone hand in hand with an increase in resistance. To track down these resistance mechanisms, scientists have turned their attention to various microbiota (gut, skin, etc.), each of which is a potential reservoir. The vaginal microbiota during pregnancy had remained largely unstudied, despite its potential importance for maternal and fetal health, until this study was published in 2026 by a French research team (Institut Pasteur, Assistance Publique–Hôpitaux de Paris, Université Paris Cité).

Resistance is common and is associated with certain bacterial species

The authors analyzed 1,957 vaginal swabs from 1,547 pregnant women: 56% of the samples contained at least one resistance gene. Which ones were the most abundant? Genes conferring resistance to the macrolide-lincosamide-streptogramin (MLS)* and tetracycline classes of antibiotics. And the most diverse? Those conferring resistance to the β-lactam class. But most importantly: genes for resistance to MLS and tetracycline-class antibiotics were found to be associated with the presence of a wide range of bacterial species, including L. iners** and G. vaginalis. For their part, Enterococcus spp., Streptococcus spp. and Staphylococcus spp. were associated with β-lactam resistance mediated by the mecA or blaZ genes. While these associations involve several species of bacteria in the vaginal microbiota, it wasn’t shown that these bacteria themselves express the genes identified.

The microbiota influences the resistome

The diversity of resistance genes depended on microbial community types (or CSTs): a vaginal microbiota dominated by L. crispatus (CST I) was associated with a scant and less diverse resistome, suggesting a more limited potential for the spread of resistance. Conversely, communities dominated by L. iners (CST III) or those that were more diverse and low in Lactobacillus (CST IV) exhibited more resistance genes and mobile genetic elements capable of carrying them, suggesting an increased potential for horizontal gene transfer between bacteria.

The vaginal resistome and obstetric complications

Lastly, the authors identified a resistome signature associated with adverse pregnancy outcomes (preterm labor or preterm delivery with rupture of membranes): this signature is characterized by an increase in Enterobacterales (particularly the bacteria E. coli and K. pneumoniae), a decrease in several Lactobacillus species, and an increase in genes conferring resistance to β-lactams, blaTEM-1 and cfxA in particular. In these women, however, this profile is not sufficient to confirm the presence of an infection. The decrease in lactobacilli is part of a change in bacterial diversity, particularly in the group with preterm premature rupture of membranes.

The vaginal microbiota thus appears to constitute a structured reservoir of antibiotic resistance genes, contributing to the human resistome overall. However, several questions remain unanswered: Are the resistance genes that are present actually expressed? Are they actually transferred between bacteria? Can they be transmitted to the newborn? These are all questions that will require functional and longitudinal studies. The findings of this team could also open up new possibilities for maternal and neonatal health, although there are no validated clinical applications at this stage.