The cervicovaginal microbiome and its resistome in a random selection of Afro-Caribbean women

Abstract

The cervicovaginal microbiome consists of community state types (CSTs) I-V. Several studies have reported positive correlations between health issues such as bacterial vaginosis (BV), acquisition of sexually transmitted infections (STIs), preterm labour and CST IV. The cervicovaginal microbiome in Afro-Caribbean women has never been characterized. Hence, this study aimed to determine the composition, CST, microbial function and resistome of the cervicovaginal microbiome in a cohort of Afro-Caribbean women using targeted (16S rRNA V4) and whole genome shotgun metagenomics. CST IV predominated in this ethnic group, with Prevotella (13.91 %) being the most abundant genus followed by Gardnerella (12.14 %). The relative abundance for Lactobacillus was 9.37 %. The most abundant species for Prevotella and Lactobacillus were P. timonensis (5.00 %) and L. iners (7.00 %), respectively. Taxa with significant nucleotide similarity to the less virulent culture collection strain G. vaginalis 409–05 (8.14 %) were more abundant than G. vaginalis ATCC 14019 (4.00 %) in this group that was asymptomatic of BV. Functional profiling revealed a high abundance of biological processes (such as flagellum-dependent cell motility, cell adhesion and quorum sensing) associated with biofilm activity. In the resistome, 2,753 predicted antimicrobial resistance (AMR) genes consisting of 28 types (mostly tet and Emr; relative abundance 52.94 % and 16.18 %, respectively) that can potentially confer resistance to tetracyclines and the macrolide-lincosamide streptogramin B group were identified. Theoretically, these AMR genes can impact the effectiveness of antibiotics commonly used in the treatment of STIs and BV. This study is the first to provide insight into the cervicovaginal microbiome and its resistome in Afro-Caribbean women.