Lactobacillus-dominated cervicovaginal microbiota associated with reduced HIV/STI prevalence and genital HIV viral load in African women

Abstract

Cervicovaginal microbiota not dominated by lactobacilli may facilitate transmission of HIV and other sexually transmitted infections (STIs), as well as miscarriages, preterm births and sepsis in pregnant women. However, little is known about the exact nature of the microbiological changes that cause these adverse outcomes. In this study, cervical samples of 174 Rwandan female sex workers were analyzed cross-sectionally using a phylogenetic microarray. Furthermore, HIV-1 RNA concentrations were measured in cervicovaginal lavages of 58 HIV-positive women among them. We identified six microbiome clusters, representing a gradient from low semi-quantitative abundance and diversity dominated by Lactobacillus crispatus (cluster R-I, with R denoting 'Rwanda') and L. iners (R-II) to intermediate (R-V) and high abundance and diversity (R-III, R-IV and R-VI) dominated by a mixture of anaerobes, including Gardnerella, Atopobium and Prevotella species. Women in cluster R-I were less likely to have HIV (P=0.03), herpes simplex virus type 2 (HSV-2; P<0.01), and high-risk human papillomavirus (HPV; P<0.01) and had no bacterial STIs (P=0.15). Statistically significant trends in prevalence of viral STIs were found from low prevalence in cluster R-I, to higher prevalence in clusters R-II and R-V, and highest prevalence in clusters R-III/R-IV/R-VI. Furthermore, only 10% of HIV-positive women in clusters R-I/R-II, compared with 40% in cluster R-V, and 42% in clusters R-III/R-IV/R-VI had detectable cervicovaginal HIV-1 RNA (Ptrend=0.03). We conclude that L. crispatus-dominated, and to a lesser extent L. iners-dominated, cervicovaginal microbiota are associated with a lower prevalence of HIV/STIs and a lower likelihood of genital HIV-1 RNA shedding.

Figure 1

Co-occurrence matrix and microbiome clustering. (a) shows the six clusters obtained by Neighborhood Co-regularized Multi-view Spectral Clustering of microarray data. The white spaces between the clusters represent samples with less than 70% probability of belonging to a cluster (see also c). The co-occurrence score reflects how many times samples co-occurred in different clustering configurations. The matrix (b) shows all 196 samples on both the x- and y-axis in the same order. Only samples with at least 70% probability of belonging to a cluster are assigned to a cluster (c).

Figure 2

Distribution of the most abundant genera per cluster. (a) shows the cumulative Co-values for the most abundant genera in each cluster in descending order. Note that BVAB1 is not included because it is not yet described at genus level. Although the final cumulative Co-value of each cluster is around 60, clusters R-I and R-II have the most uneven distribution of their most abundant genera. (b) shows these most abundant genera per cluster, and highlights the dominance of lactobacilli in clusters R-I and R-II compared with a more even distribution of anaerobic genera in the other clusters. Also, large differences in richness and total S/B ratio (abundance) are apparent, with clusters R-I and R-II containing fewer genera and lower abundance than the other clusters.

Figure 3

Bacterial composition of the microbiome clusters. (a) shows the six clusters obtained by Neighborhood Co-regularized Multi-view Spectral Clustering of microarray data. The white spaces between the clusters represent samples with less than 70% probability of belonging to a cluster. (b) Heatmap, showing normalized S/B ratios on a log₂ logarithmic scale of the most abundant species/genera per cluster, as well as species/genera that have traditionally been associated with BV and have been frequently reported in the literature. (c) BV-status of the women by Nugent score at the time of sampling. The color key is on the right. (d) The Shannon diversity index for each sample. ¹Abbreviated probe name; additional targeted species in the same genus are listed in Supplementary Information.

Figure 4

Associations between microbiome clusters and HIV/STI prevalence. Women in the Lactobacillus crispatus-dominated cluster R-I had a lower prevalence of viral STIs than women in the other clusters (P<0.01) and had no bacterial STIs (P=0.15). A trend of increasing prevalence of viral STIs in clusters with increasing bacterial diversity was found, with the lowest prevalence in cluster R-I and increasing prevalence in clusters R-II, R-V and R-III/R-IV/R-VI, respectively (P_trend<0.01). *No bacterial STIs were found in women assigned to cluster R-I. ¹Only tested at M6 in the HIV-negative cohort; data available for 61 women.