Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without Chlamydia trachomatis infection in Fiji

Pacific Islanders (PI) are a vulnerable population with a high prevalence of Chlamydia trachomatis (Ct) sexually transmitted infections and remain underrepresented in research. Here, 258 vaginal and 92 paired endocervical samples from women of diverse ethnicities in Fiji were analyzed using metagenomic shotgun sequencing. Using VALENCIA, a sub-community state type (subCST) classifier, 93 (36.04%) vaginal and 38 (41.30%) endocervical microbiomes did not match reference subCSTs. We, therefore, designed four unique subCSTs, IV-D0, IV-D1, IV-D2, and IV-E-differentially dominated by Gardnerella vaginalis, Prevotella spp., and Lactobacillus iners-to improve microbiome classifications. Ct-infected paired endocervical and vaginal microbiomes were significantly more likely to have differential species relative abundance (81.58%) than uninfected pairs (35.84%; adjusted odds ratio, 7.93; 95% confidence interval, 2.93-21.93; P < 0.0001). Among paired microbiomes, the endocervix had a significantly higher alpha diversity and independently a higher alpha diversity for high-risk human papilloma virus (HPV) types compared to low-risk and no HPV. The Ct-infected endocervical network compared to all others had smaller clusters-indicating lower species abundance and decreased weight of interactions among bacterial groups within clusters-and no interactions with potentially beneficial Lactobacillus spp. These data suggest a distinct influence on this network from Ct-infected endocervical cells. Furthermore, the high relative abundance of G. vaginalis and Prevotella spp. may generate polymicrobial biofilms that predispose to and/or promote Ct and possibly HPV persistence and pathogenicity. While these data expand on the existing repertoire of endocervical and vaginal microbiomes and fill in knowledge gaps regarding PIs, prospective studies are needed to define causal associations to develop successful interventions.