{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T08:52:31Z","timestamp":1791017551582,"version":"4.1.0"},"reference-count":56,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T00:00:00Z","timestamp":1790985600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T00:00:00Z","timestamp":1790985600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["ascpt.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Clin Pharma and Therapeutics"],"abstract":"<jats:p>\n                    Antiretroviral pre\u2010exposure prophylaxis (PrEP) is less effective in women than expected, partly because drug exposure within the female genital tract is variable and may be influenced by the vaginal microbiome. We developed an integrated pharmacometrics and machine learning framework to evaluate associations between vaginal microbiome composition and cervical antiretroviral exposure in women with human immunodeficiency virus (HIV) receiving tenofovir (TFV)\u2010, lamivudine (3TC)\u2010, or emtricitabine (FTC)\u2010containing regimens. Pharmacokinetic and microbiome data were obtained from two single\u2010center studies in Uganda and the United States. Published population pharmacokinetic models were used to estimate individual parameters by maximum a posteriori Bayesian estimation and to simulate plasma and cervical tissue exposure metrics under sexual\u2010activity\u2010driven dosing that were not studied in these trials. Microbiome diversity was assessed using alpha and beta diversity analyses. Associations between microbial genera and cervical drug exposure were evaluated using correlation analysis, differential abundance testing, and three machine learning approaches: LASSO, random forest, and XGBoost. Overall vaginal microbiome diversity was not associated with cervical exposure to TFV, 3TC, or FTC. In contrast, specific taxa\u2010level associations with cervical drug exposure were identified. For TFV,\n                    <jats:italic>Gemella<\/jats:italic>\n                    was positively associated with cervical TFV\u2010diphosphate exposure, whereas\n                    <jats:italic>Megasphaera<\/jats:italic>\n                    and\n                    <jats:italic>Falsiporphyromonas<\/jats:italic>\n                    were negatively associated across multiple models. For 3TC,\n                    <jats:italic>Dialister, Prevotella, Atopobium, Streptobacillus<\/jats:italic>\n                    , and\n                    <jats:italic>Gardnerella<\/jats:italic>\n                    were repeatedly identified. For FTC,\n                    <jats:italic>Bifidobacteriaceae<\/jats:italic>\n                    was consistently selected, with\n                    <jats:italic>Lachnospiraceae<\/jats:italic>\n                    and\n                    <jats:italic>Prevotellaceae<\/jats:italic>\n                    also implicated. This pharmacometrics\u2010machine learning framework identified specific vaginal taxa associated with cervical antiretroviral exposure, supporting the future development of microbiome\u2010based biomarkers and precision PrEP strategies for women.\n                  <\/jats:p>","DOI":"10.1002\/cpt.70499","type":"journal-article","created":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T07:58:11Z","timestamp":1791014291000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Evaluating Vaginal Microbiome Effects on Antiretroviral Exposure in the Female Genital Tract Using Pharmacometric and Machine Learning Approaches"],"prefix":"10.1002","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2581-250X","authenticated-orcid":false,"given":"Diqin","family":"Yan","sequence":"first","affiliation":[{"name":"Department of Experimental and Clinical Pharmacology, College of Pharmacy University of Minnesota  Minneapolis Minnesota USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-5448-9207","authenticated-orcid":false,"given":"Lindsey B.","family":"Collins","sequence":"additional","affiliation":[{"name":"Department of Experimental and Clinical Pharmacology, College of Pharmacy University of Minnesota  Minneapolis Minnesota USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2309-0083","authenticated-orcid":false,"given":"Christopher","family":"Staley","sequence":"additional","affiliation":[{"name":"Division of Basic and Translational Research, Department of Surgery, Medical School University of Minnesota  Minneapolis Minnesota USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0046-4353","authenticated-orcid":false,"given":"Flavia Kiweewa","family":"Matovu","sequence":"additional","affiliation":[{"name":"Makerere University\u2010Johns Hopkins University Research Collaboration  Kampala Uganda"},{"name":"College of Health Sciences Makerere University  Kampala Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4145-7045","authenticated-orcid":false,"given":"Pamala","family":"Jacobson","sequence":"additional","affiliation":[{"name":"Department of Experimental and Clinical Pharmacology, College of Pharmacy University of Minnesota  Minneapolis Minnesota USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5513-5509","authenticated-orcid":false,"given":"Melanie","family":"Nicol","sequence":"additional","affiliation":[{"name":"Department of Experimental and Clinical Pharmacology, College of Pharmacy University of Minnesota  Minneapolis Minnesota USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7493-4784","authenticated-orcid":false,"given":"Shen","family":"Cheng","sequence":"additional","affiliation":[{"name":"Department of Experimental and Clinical Pharmacology, College of Pharmacy University of Minnesota  Minneapolis Minnesota USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,3]]},"reference":[{"key":"e_1_2_11_1_1","doi-asserted-by":"crossref","DOI":"10.1155\/arat\/6829446","article-title":"Advances in HIV treatment and vaccine development: emerging therapies and breakthrough strategies for long\u2010term control","volume":"2025","author":"Okesanya O.J.","year":"2025","journal-title":"AIDS Res Treat."},{"key":"e_1_2_11_2_1","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1097\/QAD.0000000000004096","article-title":"Women with HIV: increased need for reproductive health services to improve health outcomes","volume":"39","author":"Cohn S.E.","year":"2025","journal-title":"AIDS"},{"key":"e_1_2_11_3_1","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.3004006","article-title":"Emtricitabine\u2010tenofovir concentrations and pre\u2010exposure prophylaxis efficacy in men who have sex with men","volume":"4","author":"Anderson P.L.","year":"2012","journal-title":"Sci. Transl. Med."},{"key":"e_1_2_11_4_1","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1056\/NEJMoa1202614","article-title":"Preexposure prophylaxis for HIV infection among African women","volume":"367","author":"Van Damme L.","year":"2012","journal-title":"N. Engl. J. Med."},{"key":"e_1_2_11_5_1","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1056\/NEJMoa1402269","article-title":"Tenofovir\u2010based preexposure prophylaxis for HIV infection among African women","volume":"372","author":"Marrazzo J.M.","year":"2015","journal-title":"N. Engl. J. 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Lessons from the past and a roadmap for the future","volume":"101","author":"Darwich A.","year":"2017","journal-title":"Clin. Pharmacol. Ther."},{"issue":"1","key":"e_1_2_11_53_1","article-title":"A full model estimation approach for covariate effects: inference based on clinical importance and estimation precision","volume":"6","author":"Gastonguay M.R.","year":"2004","journal-title":"AAPS J."},{"key":"e_1_2_11_54_1","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1002\/psp4.12741","article-title":"An introduction to the full random effects model","volume":"11","author":"Yngman G.","year":"2022","journal-title":"CPT Pharmacometrics Syst. 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