Longitudinal impact of PrEP use and BV treatment on vaginal microbiota in adolescent girls and young women at high risk of acquiring HIV in KwaZulu-Natal.

Abstract

Background: The HIV epidemic in South Africa, particularly in high-burden regions such as KwaZulu-Natal, remains a significant public health challenge, with persistently high prevalence and incidence rates, especially among young women. The vaginal microbiome plays a crucial role in modulating HIV susceptibility and influencing the efficacy of preexposure prophylaxis (PrEP). However, little is known about the longitudinal impact of oral tenofovir disoproxil fumarate and emtricitabine (TDF-FTC) PrEP on the vaginal microbiome,nor the mechanisms by which specific bacterial taxa may modulate the pharmacokinetics and effectiveness of topical tenofovir gel. Additionally, the effects of vaginal insertion products (VIPs) and recent sexual activity on microbial composition, genital inflammation, and HIV susceptibility remain poorly understood. Methods: Chapter 2 examined the longitudinal effects of daily oral PrEP on the vaginal microbiota in 100 women enrolled in the CAPRISA 082 and 084 trials, with swabs collected at baseline, 3 months, and 6 months for 16S rRNA sequencing. Chapter 3 evaluated the relationship between cervicovaginal tenofovir (TFV) concentrations and microbial community state types (CSTs) in 69 women from the CAPRISA 008 trial, where TFV levels were measured by LC-MS/MS and microbiota composition was analyzed using 16S sequencing. In Chapter 4, the vaginal microbiomes of 219 adolescent girls and 107 adult women from the MIST cohort study were examined, with cytokine levels and immune activation assessed via multiplex bead array and T-cell analysis. All data were analyzed using R and SAS, linking microbiome composition, immune responses, and HIV prevention strategies. Results: In Chapter 2, we observe that only 8% (3/36) of women in the non-PrEP group and 13% (8/64) in the PrEP group had L. crispatus-dominated microbial communities. We investigate the dynamics of microbial community transitions over time, finding no significant difference in the rate or pattern of these transitions between the PrEP and non-PrEP groups. While Lactobacillus iners-dominated communities were less likely to transition, those that did tended to shift towards communities associated with bacterial vaginosis (BV) and increased HIV risk, independent of PrEP or antibiotic use. These findings suggest that microbial community stability and shifts towards BV-associated states are significant in the context of HIV risk, irrespective of PrEP use. In Chapter 3, we extend this exploration by examining the influence of vaginal microbiota on tenofovir (TFV) concentrations. We found that bacterial taxa distributions and community state types (CSTs) were similarly represented in both high and low TFV concentration groups. Additionally, there were no significant differences in the median log TFV concentrations between women with CST IV or Lactobacillus-dominated CSTs (p>0.005). This suggests that while vaginal microbiota composition influences several aspects of vaginal health, it does not significantly impact TFV absorption or concentration in this cohort. Chapter 4 shifts focus to the vaginal microbiome of South African adolescent girls and adult women who use vaginal insertion products (VIPs). The study reveals regional differences in hygiene practices, with women from the Western Cape predominantly using soap and water, while a substantial proportion of women in KwaZulu-Natal utilised VIPs for both hygiene and sexual enhancement. The vaginal microbiome of adolescent girls was predominantly dominated by L. iners and BV-associated communities, a profile also observed in adult women. Non-users of VIPs displayed higher levels of pro-inflammatory cytokines (MIP-1β, MIP-1α, IFN-α, IL-6, G-CSF), while VIP users demonstrated elevated levels of IFN- α and G-CSF, which could indicate an immune response to alterations in the vaginal microbiome. Conclusion: This dissertation demonstrates that the initiation of PrEP does not significantly alter vaginal microbiota or influence tenofovir concentrations, underscoring the critical role of adherence and timely application in achieving effective HIV prevention. The study concluded that vaginal microbiota diversity and sexual activity timing significantly influenced immune responses. These findings highlight the complex interplay between microbiota composition, sexual behaviour, and immune modulation in HIV susceptibility. Further investigation is warranted to identify the underlying biological mechanisms mediating these effects, such as hormonal fluctuations, mucosal repair processes following intercourse, and functional changes in the vaginal microbiome.