Effect of Azithromycin treatment on the microbial composition, functional dynamics and resistomes of endocervical, vaginal and rectal microbiomes of women in Fiji withChlamydia trachomatisinfection

Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes withChlamydia trachomatis(Ct) infection remain poorly understood. Some data exist on vaginal microbiomes pre- and post-treatment, but none are available for the endocervix or rectum that are primary sites of infection. We applied metagenomic shotgun sequencing to vaginal, endocervical and rectal samples from women who, overtime, hadCtpersistence, clearance, or no infection to evaluate azithromycin-induced changes in microbial composition, function, and the resistome. Our results show a shift in composition and function that supportCtpost-treatment with azithromycin resistance mutations in theCt rplV gene and significant endocervical enrichment of azithromycin resistance genes inLactobacillus inersandGardnerella vaginalis, the strains of which have moderate/high potential for biofilm formation. These findings highlight the unintended ecological consequences of azithromycin, including resistance gene propagation and microbiome shifts that support persistent/recurrentCt, emphasizing the need for novel treatment and microbiome- preserving strategies.