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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, had\n                  <jats:italic>Ct<\/jats:italic>\n                  persistence, 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 support\n                  <jats:italic>Ct<\/jats:italic>\n                  post-treatment with azithromycin resistance mutations in the\n                  <jats:italic>Ct rpl<\/jats:italic>\n                  V gene and significant endocervical enrichment of azithromycin resistance genes in\n                  <jats:italic>Lactobacillus iners<\/jats:italic>\n                  and\n                  <jats:italic>Gardnerella vaginalis<\/jats:italic>\n                  , 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\/recurrent\n                  <jats:italic>Ct<\/jats:italic>\n                  , emphasizing the need for novel treatment and microbiome- preserving strategies.\n                <\/jats:p>","DOI":"10.1101\/2025.04.02.646699","type":"posted-content","created":{"date-parts":[[2025,4,3]],"date-time":"2025-04-03T02:03:11Z","timestamp":1743645791000},"source":"Crossref","is-referenced-by-count":1,"title":["Effect of Azithromycin treatment on the microbial composition, functional dynamics and resistomes of endocervical, vaginal and rectal microbiomes of women in Fiji with\n                  <i>Chlamydia trachomatis<\/i>\n                  infection"],"prefix":"10.64898","author":[{"given":"Sankhya","family":"Bommana","sequence":"first","affiliation":[{"name":"Department of Pediatrics, University of California San Francisco, Oakland, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olusola","family":"Olagoke","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Francisco, Oakland, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Juan","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roselle","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Francisco, Oakland, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mike","family":"Kama","sequence":"additional","affiliation":[{"name":"Ministry of Health and Medical Services, Suva, Fiji"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morgan","family":"Dehdashti","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Francisco, Oakland, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reshma","family":"Kodimerla","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Francisco, Oakland, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy D.","family":"Read","sequence":"additional","affiliation":[{"name":"Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deborah","family":"Dean","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Francisco, Oakland, CA, USA"},{"name":"Department of Medicine, University of California San Francisco, San Francisco, CA, USA"},{"name":"Department of Bioengineering, Joint Graduate Program, University of California San Francisco and University of California Berkeley, San Francisco, CA, USA"},{"name":"Bixby Center for Global Reproductive Health, University of California San Francisco, San Francisco, CA, USA"},{"name":"Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041201532450000_2025.04.02.646699v2.1","unstructured":"Chlamydia Fact Sheet. 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