Case subjects (n= 187) were selected based on identification of an incident CT infection diagnosed during routine clinical screening with the Gen-Probe APTIMA test. Controls (n= 373) were matched to cases (2:1, respectively) at the time of incident CT infection based on age, date of study enrollment, and prior history of CT infection. Retrospective cervicovaginal swab samples were retrieved from prior visits for all participants (approximately 6 months for both cases and controls). Post-treatment samples were collected in 504/560 participants (approximately 8 months after case CT infection treatment). All cervical samples underwent 16SV4 rRNA and ITS1 amplicon sequencing for assessment of bacteria and fungi/eukaryotes, respectively. HPV genotyping was analyzed using data from the parent study and included high-risk (oncogenic) HPV typesHPV16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, and -59. Multivariate modeling was used to determine (1) prospective risk of CT acquisition (at t1), (2) the association of CT infection and the CVM (at t0), and (3) residual effects of treated CT infection on the CVM (at t+1).
