Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased HIV Acquisition in Young South African Women

Abstract

Elevated inflammation in the female genital tract is associated with increased HIV risk. Cervicovaginal bacteria modulate genital inflammation; however, their role in HIV susceptibility has not been elucidated. In a prospective cohort of young, healthy South African women, we found that individuals with diverse genital bacterial communities dominated by anaerobes other than Gardnerella were at over 4-fold higher risk of acquiring HIV and had increased numbers of activated mucosal CD4⁺ T cells compared to those with Lactobacillus crispatus-dominant communities. We identified specific bacterial taxa linked with reduced (L. crispatus) or elevated (Prevotella, Sneathia, and other anaerobes) inflammation and HIV infection and found that high-risk bacteria increased numbers of activated genital CD4⁺ T cells in a murine model. Our results suggest that highly prevalent genital bacteria increase HIV risk by inducing mucosal HIV target cells. These findings might be leveraged to reduce HIV acquisition in women living in sub-Saharan Africa.

Keywords: HIV acquisition; HIV susceptibility; female genital tract (FGT); mucosal immunology; sub-Saharan Africa; vaginal microbiome.

Figure 1. Bacterial, but not viral, cervicovaginal community structures are distinct in HIV-uninfected women

(A) Stacked bar plot indicating the bacterial composition of the cervicovaginal microbiome of 236 HIV-uninfected women. Samples were grouped according to 4 cervicotypes (CTs), and the alpha diversity is shown below for each sample. (B) Principal coordinates analysis (PCoA) plot of the 236 individuals, distinguished by CT. (C) Normalized reads of alphapapillomaviruses and Anelloviridae detected in CVL fluid, grouped by CT (n=180 individuals). Groups were compared using Kruskal-Wallis test. The percentage of samples in which the indicated virus was detected is shown below. (D) Average linkage clustering of the Bray-Curtis dissimilarity of relative abundances of Caudovirales sequences detected in CVL fluid (n=180 individuals). Lines in the plots indicate the median and the interquartile range (IQR) of the dataset.

Figure 2. Cervicovaginal bacteria impact HIV acquisition

(A) Kaplan-Meier curve showing HIV infections in each CT group over time, including or excluding individuals with Chlamydia infection. Acquisition curves for CT2 (n=74/65 individuals), CT3 (n=68/57) and CT4 (n=68/54) were compared with the acquisition curve for CT1 (n=23/23). Log-rank (Mantel-Cox) test-based p values and Mantel-Haenszel hazard ratios (HR) are displayed. (B) Distribution of CT groups in participants who remained HIV-uninfected (n=205) versus those who acquired HIV (n=31), shown as % of total, and the difference in distribution between these two groups. (C) Stacked bar plot indicating the bacterial composition of the cervicovaginal microbiome of 31 women who subsequently acquired HIV. Samples were grouped by CT. (D) Bacterial PCoA plot indicating study participants who acquired HIV (in red, n=31) and CT groups for those who remained HIV-uninfected (faded coloring, n=205). See also Figure S1 and Table S1.

Figure 3. High-risk genital bacterial communities are associated with increased HIV target cell numbers and pro-inflammatory cytokines

(A) Representative flow cytometry plots to identify HIV target cells isolated from cervical cytobrushes. Live T cells (CD45⁺CD3⁺) were gated on cells expressing CD4, HLA-DR, CD38 and CCR5. (B) Flow cytometry analysis of HIV target cell numbers in cytobrushes from 169 individuals, grouped by CT. (C,D,E) Chemokine and cytokine concentrations in CVL fluid from 219 individuals, grouped by CT. The bottom figure panel in (D) further distinguishes between samples of women who became infected with HIV and those who remained HIV-uninfected. Lines indicate the median and the interquartile range (IQR) of each dataset. Groups were compared using Kruskal-Wallis test with Dunn’s post-hoc analyses. See also Figures S2 and S3.

Figure 4. Specific bacterial taxa are associated with genital inflammation and HIV infection

(A) Bacterial taxa in 219 individuals positively or negatively correlated with cytokine principal component 1 (PC1), an indicator of the presence of genital inflammation. Q-values reflect corrected p-values after multiple testing. (B) Cytokine and chemokine concentrations measured in the supernatant of cervical epithelial cells co-cultured with the indicated bacteria for 24 h (pooled results from 2–3 independent experiments; Kruskal-Wallis test). (C) Bacterial taxa significantly differentially abundant in women who became infected with HIV (n=31) and those who remained uninfected (n=205), including two strains of P. bivia. Error bars indicate the standard error estimate for the log2 fold change in abundance. (D) Germ-free mice were intravaginally inoculated with L. crispatus or P. bivia on day 0 and day 2 and sacrificed on day 6. (E) Numbers of activated (CD44⁺) CD4⁺ T cells detected in the female genital tract (FGT) and in 100 μl blood of the gnotobiotic mice on day 6 of the experiment (pooled results from 3 independent experiments; Mann-Whitney test). Lines in the plots indicate the median and the interquartile range (IQR) of the dataset. See also Figure S4.