Exploring the Vaginal Microbiome During Pregnancy: Microbial Diversity, E. coli pathogenicity, and Links to Urinary Tract Colonization

Abstract This study explores the role of the vaginal microbiota (VM) in the pathophysiology of asymptomatic bacteriuria (ASB), which requires systematic screening and antibiotic treatment during pregnancy. We hypothesize that disruptions in the VM composition may promote the ascending colonization of bacteria from the gut to the urinary tract, reinforcing the existence of a gut-urogenital axis. A healthy VM is typically characterized by low diversity and is dominated by lactic acid-producing species, notably those from the Lactobacillus genus. Diversity analyses of whole genomes metagenomic sequencing data from 1,553 pregnant women revealed a metagenomic signature characterized by an increase in phylogenetic diversity within the VM during ASB. This shift includes both a decrease in lactobacilli and an increase in the abundance of taxa associated with the gut microbiota, particularly Enterobacterales, with a substantial rise in Escherichia coli abundance. Worldwide, E. coli remains the most common etiological agent of bacteriuria during pregnancy and also a major causative agent of newborn infections. Given its importance and the limited data on its characterization within the VM during pregnancy, we performed genomic assembly and analysis of this species from pregnant women of this cohort. Molecular typing and antimicrobial resistance characterization of 72 assembled E. coli genomes revealed a genomic signature of Extra-Intestinal pathogenic E. coli (“ExPEC”) strains, which are involved in various extraintestinal infections such as urinary tract infections, newborn infections and bacteremia. Moreover, the presence of this species in the vaginal environment was associated with a substantial variation of the microbial diversity, primarily marked by a decrease in abundance of Lactobacillus species. Overall, our study shows how disruption in key bacterial group within the VM can disrupt its stability, potentially leading to the colonization by opportunistic pathogens.