Background: Sexual transmission of the urogenital microbiota may contribute to adverse outcomes. However, the extent of sexual transmission of urogenital bacterial strains is unclear as prior studies largely investigated specific pathogens. We used epidemiologic and whole metagenome sequencing data to characterize urogenital microbiome strain concordance between sexual contacts.
Methods: Individuals attending STI clinics in the Baltimore, Maryland metropolitan area who tested positive for genital Chlamydia trachomatis (CT, nucleic acid amplification test) were enrolled and referred their sexual contacts from the prior 60 days. Snowball recruitment of prior-60-day sexual contacts continued for up to four waves. Endocervical brush and urethral swab samples were collected from female and male participants, respectively, and used for whole metagenome sequencing. Metagenomes were assembled using metaSPAdes and binned using a reference-guided approach. Bacterial strain concordance was evaluated using inStrain and network analysis.
Results: Of 139 participants, 75 (54%) were female, 121 (89%) had genital CT, and 42 (30%) were recruited contacts. We identified 63 strain-concordance events among 40 participants; 11 events (17%) were between sexual contacts. Concordant strains represented 13 species, including Lactobacillus spp., bacterial vaginosis (BV)-associated taxa, and CT. There were a median of 40 single nucleotide polymorphisms per megabasepair (SNP/Mbp) between concordant strains (range 0–99). The distribution of SNP/Mbp between concordant strains differed between species and by whether strains were concordant between sexual contacts (Kruskal Wallis p=0.02, p=0.004, respectively). Prevotella timonensis, Sneathia amnii, and Sneathia sanguinegens strains had <2 SNP/Mbp when shared between heterosexual contacts. One L. iners strain shared between female sexual contacts had 1 SNP/Mbp. This was the only Lactobacillus strain shared between sexual contacts. These data likely underestimate strain sharing between sexual contacts because low biomass was recovered from many male urethral swabs.
Conclusions: These data provide evidence of heterosexual transmission of P. timonensis, S. amnii, and S. sanguinegens, which may promote persistent and recurrent BV among female partners. These findings inform design and improved efficacy of partner-treatment interventions to reduce BV recurrence. These data also demonstrate frequent strain concordance between female non-contacts, which reflects co-membership in a larger sexual network and limited geographical intraspecies diversity.
