Comparative analysis of vaginal microbiota sampling using menstrual cups and high vaginal swabs in pregnant women living with HIV-1 infection

Objective: To compare the efficacy of menstrual cups and high vaginal swabs (HVS) in collecting bacterial biomass for 16S rRNA gene amplicon sequencing. Samples: Cervicovaginal fluid samples from 16 HIV-1 infected pregnant women. Method for endpoints: Samples were taken with both HVS and menstrual cups, followed by DNA extraction, bacterial 16S RNA amplicon sequencing, and data analysis using MOTHUR, MicrobiomeAnalyst, SPSS, and R. The total DNA, bacterial load, amplicon read counts, diversity matrices, and bacterial taxa were compared. Main Result: Both menstrual cups and HVS are suitable for assessing vaginal microbiota composition and diversity in HIV-1 pregnant individuals, with menstrual cups offering some advantages like higher total sample volume.