Data on the composition and structure of the vaginal microbiome in women with genital Chlamydia trachomatis published in The Journal of Infectious Diseases revealed that Lactobacillus iners– dominated communities were most common post-treatment.

Investigators recruited a cohort of 149 women with C trachomatis at baseline who were followed quarterly for 9 months following antibiotic treatment. Most patients were African American (86%), and the ages ranged from 13 to 33 years. Participants provided a total of 141 microbiome samples at the baseline visit. The women were then treated with a 1-g single dose of azithromycin and additional samples were collected at 3-, 6- and 9-months post-treatment.

Seventeen participants tested positive for C trachomatis at 3 months post-treatment follow-up, 12 patients tested positive at 6 months, and 14 were positive at 9 months. At the time of diagnosis, vaginal microbiota was dominated by L iners or a diverse array of bacteria associated with bacterial vaginosis including Gardnerella vaginalis, Atopobium vaginae, or Mobiluncus curtisii. Posttreatment, researchers found that vaginal microbiota commonly showed a relative abundance of L iners communities, which according to investigators, is consistent with the observed relative resistance of L iners to the highest concentrations of azithromycin.

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It is important to note that the inclusion criteria focused on women with C trachomatis at baseline, and therefore it is not possible to determine whether overrepresented bacterial phylotypes or community state types at visit 1 were present before infection. Investigators were also unable to distinguish between C trachomatis clearance or antibiotic treatment as the causal determinant in microbiota composition. They further cautioned that, “studies of the vaginal microbiota during prevalent [C trachomatis] infection do not resolve whether the observed microbiota is causal to the increased risk of [C trachomatis] infection, or if it is a consequence of [such] infection.”

The study also lacked sufficient power to detect statistically significant effects of reinfection at visit 3 and 4. Further, the control group recruited was exclusively comprised of healthy African American women and girls, while the study cohort was not; therefore, investigators could not exclude differences as a result of confounding characteristics.

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The results of the study confirmed the association between C trachomatis infection and non-Lactobacillus species of microbiota, as well as that microbiota is commonly dominated by L iners. In addition, high-risk infection may be maintained in part by antibiotic treatment. According to investigators, “our results stress the importance of taking into account the potential perturbing effects of antibiotic treatment on the vaginal microbiota, whether it is for the treatment of [C trachomatis] infections or other indications.” Investigators also highlighted an urgent need for studies of the effect of antibiotic therapy on the composition of the vaginal microbiota, which could aid in the development of strategies to protect and restore optimal vaginal microbiota.


Tamarelle J, Ma B, Gajer P, et al. Nonoptimal vaginal microbiota after azithromycin treatment for Chlamydia trachomatis infection [published online October 1, 2019]. J Infect Dis. doi:10.1093/infdis/jiz499