Water source, latrine type, and rainfall are associated with detection of non-optimal and enteric bacteria in the vaginal microbiome: a prospective observational cohort study nested within a cluster randomized controlled trial

Abstract

Background: Less than one-third of sub-Saharan Africans have access to improved water sources. In US, Indian, and African studies, Bacterial vaginosis (BV) is increased among women with poor water, sanitation, and hygiene (WASH). We examined water source, sanitation (latrine type), and rainfall in relation to the vaginal microbiome (VMB).

Methods: In a cluster randomized controlled trial of menstrual cups and cash transfer, we measured the impact of cups on VMB via 16S rRNA gene amplicon sequencing in a subset of 436 adolescent girls. We analyzed how self-reported water source and latrine type at home related to VMB over 18-months, examining community state type I (CST-I, L. crispatus dominant) vs. other CST; alpha diversity; targeted taxa (coliform and other water-related pathogens); and non-targeted taxa via machine learning approaches. Mixed effects multivariable longitudinal models were adjusted for intervention arm, age, socioeconomic status, sexual activity, and cluster-level school WASH and rainfall (in millimeters).

Results: Adjusting for all covariates in all models: (1) the odds of CST-I were increased among participants with piped water (vs. pond), and decreased with traditional pit latrine vs. flush toilet. (2) Alpha diversity varied by water source and latrine type without consistent trends. (3) Coliform bacteria relative abundance (RA) was higher among participants with traditional pit or ventilated improved pit latrines vs. flush toilet, and higher among participants relying on stream vs. pond water. Streptococcus agalactiae RA was higher among participants with non-flush toilets, while Bacteroides fragilis RA was lower with non-flush toilets. (4) Key taxa from non-targeted analyses associated with water source and latrine type included typical vaginal bacteria, opportunistic pathogens, and urinary tract pathobionts. (6) Increased rainfall was associated with decreased odds of CST-I.

Trial registration: ClinicalTrials.gov NCT03051789, February 14, 2017.

Keywords: Bacterial vaginosis; Climate change; Latrine; Menstrual hygiene management; Vaginal microbiome; WASH; Water; Water sanitation and hygiene.

Fig. 1

Distribution of vaginal community state type and shannon diversity index by water source and latrine type over time. Legend: Color shading and intensity represent proportions of optimal community state type-I (CST-I; L. crispatus dominant) and Shannon diversity index (SDI) by category of water source and latrine type. A lower proportion of observations CST-I and higher Shannon diversity index are represented with red shades, and a higher proportion of CST-I and lower Shannon diversity index are represented with green shades, with medium values transitioning through yellow. Thus, for example, participants with piped water in the home consistently have the highest proportion of observations with CST-I, while those relying on bush/field for latrine type consistently have the lowest proportion of observations with CST-I. Alpha diversity, as represented here by Shannon diversity index, is less consistent over visits

Fig. 2

Results of multivariable alpha diversity analyses. Legend: The results of multivariable mixed effects linear regression are summarized in the plots above for alpha diversity measures: (A) Shannon diversity index and (B) Richness. Coefficients are represented with black diamonds, and 95% and 90% Confidence Intervals (CI) in blue bars, as shown in the legend. Models are simultaneously adjusted for all variables presented. For water sources, the reference is “pond” and for latrine type the reference is “flush toilet”

Fig. 3

Results of mixed effects multivariable poisson regression: targeted taxa association with water source and latrine type. Legend: Heatmap summarizing prevalence rate ratios (PRRs) for the associations between water source, latrine type, and other covariates in relation to the targeted taxa. The heatmap represents the direction and magnitude of the PRR for the covariates. PRRs < 1 (i.e., inverse relationship) are shaded in blue, and positive PRRs (> 1) are shaded in green to red, with deeper intensity representing the magnitude of the association. Covariate associations with p-value < 0.10 are shown in color, and those with p-value < 0.05 are indicated with an asterisk (*). Covariates associations that are not significant but maintained in the model for fit are shown in light grey. White space indicates the variable is not included in the model. For water sources, the reference is “pond” and for latrine type the reference is “flush toilet”