Nonoptimal Vaginal Microbiota After Azithromycin Treatment for Chlamydia trachomatis Infection

Abstract

We characterized the composition and structure of the vaginal microbiota in a cohort of 149 women with genital Chlamydia trachomatis infection at baseline who were followed quarterly for 9 months after antibiotic treatment. At time of diagnosis, the vaginal microbiota was dominated by Lactobacillus iners or a diverse array of bacterial vaginosis-associated bacteria including Gardnerella vaginalis. Interestingly, L. iners-dominated communities were most common after azithromycin treatment (1 g monodose), consistent with the observed relative resistance of L. iners to azithromycin. Lactobacillus iners-dominated communities have been associated with increased risk of C. trachomatis infection, suggesting that the impact of antibiotic treatment on the vaginal microbiota could favor reinfections. These results provide support for the dual need to account for the potential perturbing effect(s) of antibiotic treatment on the vaginal microbiota, and to develop strategies to protect and restore optimal vaginal microbiota.

Keywords: Chlamydia trachomatis; 16S rRNA gene sequencing; antibiotics; longitudinal; sexually transmitted infection; vaginal microbiome.

Figure 1.

Heatmap representing the relative abundance of the 20 most abundant phylotypes found in the vaginal microbiota of 395 samples collected every 3 months for 9 months after azithromycin treatment for Chlamydia trachomatis by 149 young females in the Chlamydia Adolescent/Adult Reproductive Management prospective cohort, Baltimore, Maryland, and 99 samples from 99 women enrolled in the VM400 cross-sectional control study, Baltimore, Maryland [30]. Ward linkage clustering was used to cluster samples based on their Euclidian distance calculated in the “vegan” package in R. The 4 bars on top indicate community state types, according to the previous naming convention [30], Nugent Score, vaginal pH, and visit number. Abbreviations: BVAB, bacterial vaginosis–associated bacteria; CHARM, Chlamydia Adolescent/Adult Reproductive Management; CST, community state types.

Figure 2.

Proportions of community state types (CSTs) in Chlamydia Adolescent/Adult Reproductive Management (CHARM) samples from visit 1 (Chlamydia trachomatis [CT] positive) and visit 2 (CT negative, 3 months posttreatment) and in VM400 controls.

Figure 3.

Community state type (CST) proportions in Chlamydia Adolescent/Adult Reproductive Management (CHARM) samples from visit 1 (Chlamydia trachomatis [CT] positive, pretreatment), visit 2 (CT negative only, 3 months posttreatment), visit 3 (CT negative only, 6 months posttreatment), and visit 4 (CT negative only, 9 months posttreatment) and in VM400 controls.

Figure 4.

Volcano plots displaying results of negative binomial regression model using the DESeq2 package on R [29], comparing phylotypes differentially expressed between Chlamydia Adolescent/Adult Reproductive Management (CHARM) samples: visit 1 (Chlamydia trachomatis [CT] positive) to visit 2 (CT negative) (A), visit 2 (CT negative) to visit 3 (CT negative) (B), visit 3 (CT negative) to visit 4 (CT negative) (C), for phylotypes present in at least 20% of samples for each analysis (33, 32, and 34 phylotypes, respectively). The log₂ fold change is plotted against the –log₁₀ of the Q value, which is the P value corrected for multiple testing using Benjamini–Hochberg correction (BH). Positive values of the log₂ fold change indicate phylotypes overrepresented in the first visit of the 2 visits considered, whereas negative values indicate phylotypes overrepresented in the second visit.

Figure 5.

Antimicrobial susceptibility test of 5 major vaginal bacterial species for azithromycin and doxycycline. Minimum inhibitory concentration (MIC) was determined by broth microdilution protocol [32] with concentrations ranging from 0.016 µg/mL to 256 µg/mL. Number of strains tested: Gardnerella vaginalis: 8; Lactobacillus crispatus: 6; Lactobacillus gasseri: 5; Lactobacillus iners: 10; Lactobacillus jensenii: 3.

Figure 6.

Transitions between community state types (CSTs) from one visit to another in Chlamydia Adolescent/Adult Reproductive Management (CHARM) samples. A, Individual trajectories of women included in the study. B, CST transitions from Chlamydia trachomatis (CT)–positive samples pretreatment to CT-negative samples posttreatment at 2 consecutive visits. C, CST transitions among CT-negative samples at 2 consecutive visits. D, CST transitions from CT-negative samples to CT-positive samples at 2 consecutive visits. The number next to a line represents the number of women transitioning from one CST to another. Looped arrows represent the number of women staying in the same CST between 2 visits and are colored green. In B, C, and D, circle size is proportional to total frequency of CSTs.