Chlamydia trachomatis (CT) is the most common bacterial sexually transmitted infection. In the U.S., women
aged 15-24 have the highest CT burden: 782,697 cases in 2019. Up to 80% of urogenital CT infections are
asymptomatic, and untreated persistent infection can cause pelvic inflammatory disease, infertility, and ectopic
pregnancy. Risk of reproductive sequelae rises with duration of CT persistence, likely due to chronic inflammation
in the fallopian tubes. In contrast, untreated CT can spontaneously clear without antibiotic use. Clearance rate
estimates vary: it appears 7-44% of women clear CT between testing and initiating treatment (~1-2 weeks), but
mechanisms of this natural resolution are poorly understood. Studies show spontaneous clearance may reduce
reinfection, and antibiotics may impede development of lasting immunity. We have strong preliminary data that
bacterial vaginosis, a condition characterized by a low-Lactobacillus vaginal microbiota, is associated with CT
persistence. This project will further identify specific features of the vaginal metagenome and immune
milieu that contribute to spontaneous CT clearance and assess if these features differ by infection
duration. Antibiotic-sparing approaches to promote CT clearance will offer the most protection from reproductive
sequelae when clearance is rapid and occurs early in infection. The proposed work will leverage a unique set of
cervicovaginal lavage samples from a large longitudinal study (n=1,053 samples, n=431 women). Quarterly
samples were collected for 1 year. Due to historical reasons, a majority of the samples were screened for CT at
study end. We identified 310 spontaneous clearance events: 247 were rapid and 63 delayed. Clearance events
were matched to control persistence events on infection duration. This proposal focuses on epidemiologically
robust analyses of the vaginal metagenome and immune milieu at CT+ visits (before clearance) to identify
features that may functionally contribute to clearance. Specific aims will evaluate whether the following are
associated with spontaneous CT clearance and if associations differ by infection duration: (1) species- and strain-
specific vaginal bacteria growth rates, (2) interplay of Th1 and Th17 immune responses, and (3) interactions
between the vaginal metagenome and immune milieu. Bacterial growth rates may reflect metabolic activity and
allow identification of bacteria that functionally contribute to CT clearance. Spontaneous clearance is likely
mediated by IFN¿ and Th1 immune responses; Th17 responses may promote persistence and pathology.
However, data suggest IFN¿’s role in clearance may depend on timing and duration of its production, and Th17
and Th1 responses may regulate each other. The microbiome and host constantly interact, and multi-omic
analyses of microbiome and host immune data can yield insights that are missed in single-omic analyses. This
work will highlight potential targets to promote rapid CT clearance, which can be validated in vitro and translated
into interventions. It will also inform CT vaccine design by characterizing immune responses that promote rapid
clearance. This F32 will provide postdoctoral training in metagenomic, immune marker, and multi-omic analyses.
