Rapid and Profound Shifts in the Vaginal Microbiota Following Antibiotic Treatment for Bacterial Vaginosis

Abstract

Background: Bacterial vaginosis (BV) is a common polymicrobial disease associated with numerous negative reproductive health outcomes, including an increased risk of human immunodeficiency virus acquisition. BV is treatable with antibiotics, but relapse is common. A more detailed understanding of bacterial dynamics during antibiotic therapy for BV could identify conditions that favor establishment, maintenance, and eradication of BV-associated bacterial species, thereby improving treatment outcomes.

Methods: We used mathematical models to analyze daily quantitative measurements of 11 key bacterial species during metronidazole treatment for 15 cases of BV.

Results: We identified complete reorganization of vaginal bacterial composition within a day of initiating therapy. Although baseline bacterial levels predicted a longer time to clearance, all anaerobic species were eliminated rapidly within a median of 3 days. However, reemergence of BV-associated species was common following treatment cessation. Gardnerella vaginalis, a facultative anaerobe, was cleared more slowly than anaerobic BV-associated species, and levels of G. vaginalis often rebounded during treatment. We observed gradual Lactobacillus species growth, indicating that untargeted microbes fill the transient vacuum formed during treatment.

Conclusions: Under antibiotic pressure, the human microbiome can undergo rapid shifts on a scale of hours. When treatment is stopped, BV-associated bacteria quickly reemerge, suggesting a possible role for intermittent prophylactic treatment.

Keywords: Gardnerella vaginalis; Lactobacillus; bacterial vaginosis; mathematical modeling; metronidazole; qPCR; vaginal microbiota.

Figure 1.

Pretreatment ranges for bacterial concentration during bacterial vaginosis. Distributions of pretreatment log₁₀16S ribosomal RNA (rRNA) gene copies/swab for each measured bacterium, ordered by increasing mean. Boxes represent the interquartile range (IQR) of the data, the whiskers extend to cover all data within 1.5 times the IQR of the first or third quartile, and solid dots represent outliers. Sample sizes at baseline are given for each species (out of 15 total episodes). Lactobacillus jensenii was removed because of small sample size (n = 1 with a baseline log₁₀ 16S rRNA count of 6.40 gene copies/swab). Abbreviations: A. vaginae, Atopobium vaginae; BVAB, BV-associated bacterium; G. vaginalis, Gardnerella vaginalis.

Figure 2.

Time until suppression for bacterial vaginosis (BV)–associated bacteria during metronidazole therapy according to pretreatment bacterial concentration. A, Distributions of total treatment days until suppression for each BV-associated bacterium (BVAB). Bacteria are listed in order of increasing pretherapy mean. Boxes represent the interquartile range (IQR) of the data, the whiskers extend to cover all data within 1.5 times the IQR of the first or third quartile, and circles represent raw data. Sample sizes are given below the box plots. B, Scatterplot of log₁₀ baseline counts versus treatment days until bacterial suppression. Gardnerella vaginalis is not included because of low numbers of participants with complete suppression (3 total on days 1, 3, and 8). Colors of dots correspond to colors of box plots in panel A. Abbreviations: A. vaginae, Atopobium vaginae; rRNA, ribosomal RNA.

Figure 3.

Individual clearance curves and clearance rate comparisons for bacterial vaginosis (BV)–associated bacteria (BVAB) during metronidazole treatment. A, Each color denotes a different participant. Only Gardnerella vaginalis is notable for frequent bacterial rebound. B, Each bubble represents the mean differences in clearance rates (log₁₀ 16S ribosomal RNA [rRNA] gene copies/swab/day) between the bacterial group listed to the left and the bacterial group listed below. Rate differences and P values were estimated using a linear mixed model. Atopobium vaginae had the fastest mean clearance rate and G. vaginalis the slowest mean clearance rate, compared with the other bacteria. Abbreviation: NS, not significant.

Figure 4.

Higher clearance half-life variability within bacterial vaginosis (BV)–associated bacterial (BVAB) species as compared to within study participants. A, Distribution of estimated bacterial clearance half-lives (days) for each BV-associated bacterial group, sorted by increasing median. B, Distributions of half-lives (days) for each participant, arranged by increasing median. Participants who received oral metronidazole treatment are denoted in red. Repeat episodes in the same subject share the same letter. Boxes represent the interquartile range (IQR) of the data, and the whiskers extend to cover all data within 1.5 times the IQR of the first or third quartile. Dots represent each individual clearance half-lives: black denotes topical metronidazole use and red denotes oral metronidazole use. Two Gardnerella vaginalis outliers are not shown (bacterial half-lives of 28 hours for episode G and 41 hours for episode A3). One episode (A3) was removed from panel B because it had only 2 data points, and 2 other episodes (B and C2) were not included owing to a lack of estimated clearance half-lives. Abbreviation: A. vaginae, Atopobium vaginae.

Figure 5.

Lactobacillus species growth during antibiotic therapy. A, Time series plots (top half) for each Lactobacillus species during antibiotic treatment (each color denotes a different participant). Loess splines (bottom half) correspond to the data in the top half of figure. B, Daily distribution of the vaginal microbiota composition (log₁₀ proportion of total bacteria), comparing bacterial vaginosis (BV)–associated bacteria (BVAB; red box plots) to Lactobacillus species (black box plots) during the observation period (sample sizes are depicted below box plots). Boxes represent the interquartile range (IQR) of the data, the whiskers extend to cover all data within 1.5 times the IQR of the first or third quartile, and solid dots represent outliers. Abbreviation: rRNA, ribosomal RNA.