Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without
Chlamydia trachomatis
infection in Fiji
Authors: Bommana Sankhya , Hu Yi-Juan , Kama Mike , Wang Ruohong , Kodimerla Reshma , Jijakli Kenan , Read Timothy D. , Dean Deborah 
Published: December 2023

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.

IMPORTANCE

Chlamydia trachomatis
(
Ct
) is the most common sexually transmitted bacterium globally. Endocervical and vaginal microbiome interactions are rarely examined within the context of
Ct
or among vulnerable populations. We evaluated 258 vaginal and 92 paired endocervical samples from Fijian women using metagenomic shotgun sequencing. Over 37% of the microbiomes could not be classified into sub-community state types (subCSTs). We, therefore, developed subCSTs IV-D0, IV-D1, IV-D2, and IV-E—dominated primarily by
Gardnerella vaginalis
—to improve classification. Among paired microbiomes, the endocervix had a significantly higher alpha diversity and, independently, higher diversity for high-risk human papilloma virus (HPV) genotypes compared to low-risk and no HPV.
Ct-
infected endocervical networks had smaller clusters without interactions with potentially beneficial
Lactobacillus
spp. Overall, these data suggest that
G. vaginalis
may generate polymicrobial biofilms that predispose to and/or promote
Ct
and possibly HPV persistence and pathogenicity. Our findings expand on the existing repertoire of endocervical and vaginal microbiomes and fill in knowledge gaps regarding Pacific Islanders.