Evaluation of patient- versus provider-collected vaginal swabs for microbiome analysis during pregnancy

Objective: We aimed to evaluate if patient- and provider-collected vaginal swabs in pregnant women reflect similar bacterial community characteristics. Pregnant patients performed a self-collected vaginal swab, then underwent a provider-collected swab via speculum exam. DNA pyrosequencing of the 16S rRNA gene V1V3 and V3V5 variable regions was performed. Relative abundance of taxa, alpha diversity, and beta diversity of patient- and provider-collected swabs were compared. Results: Ninety-four vaginal swabs from 47 women were analyzed. On non-metric multi-dimensional scaling plots, paired patient- and provider-collected swabs clustered closely. The median Pearson correlation coefficient was 0.993 (interquartile range 0.951-0.999) for V1V3 and 0.987 (interquartile range 0.902-0.999) for V3V5. Among paired V1V3 and V3V5 sequences, 83.0% and 73.9% showed strong Pearson correlation (> 0.9), respectively, between patient- and provider-collected swabs; V1V3 and V3V5 sequences with weaker Pearson correlation (< 0.9) had correlation coefficients 0.57-0.89 and 0.49-0.89, respectively. No taxa were preferentially detected by sampling method, with relative abundance of taxa highly conserved. No significant difference in Shannon diversity for V1V3 (p = 0.22) and V3V5 (p = 0.11) sequences among paired samples was seen. We demonstrate that bacterial communities defined from patient- and provider-collected vaginal swabs in pregnant women are similar, validating utilization of patient-collected swabs for vaginal bacterial microbiome sampling during pregnancy.