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Here we develop a data-driven model of the within-host dynamics of extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae. We use blaCTX-M (the most widespread ESBL gene family) and 16S rRNA (a proxy for bacterial load) abundance data from 833 rectal swabs from 133 ESBL-positive patients followed up in a prospective cohort study in three European hospitals. We find that cefuroxime and ceftriaxone are associated with increased blaCTX-M abundance during treatment (21% and 10% daily increase, respectively), while treatment with meropenem, piperacillin-tazobactam, and oral ciprofloxacin is associated with decreased blaCTX-M (8% daily decrease for all). The model predicts that typical antibiotic exposures can have substantial long-term effects on blaCTX-M carriage duration.<\/jats:p>","DOI":"10.7554\/elife.49206","type":"journal-article","created":{"date-parts":[[2020,5,7]],"date-time":"2020-05-07T05:00:35Z","timestamp":1588827635000},"source":"Crossref","is-referenced-by-count":34,"title":["Quantifying antibiotic impact on within-patient dynamics of extended-spectrum beta-lactamase resistance"],"prefix":"10.7554","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6751-4124","authenticated-orcid":true,"given":"Rene","family":"Niehus","sequence":"first","affiliation":[{"name":"University of Oxford, Oxford, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esther","family":"van Kleef","sequence":"additional","affiliation":[{"name":"National Institute for Public Health and theEnvironment, Bilthoven, 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Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evelina","family":"Tacconelli","sequence":"additional","affiliation":[{"name":"University of Tuebingen, Tuebingen, Germany"},{"name":"Infectious Diseases, University of Verona, Verona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Biljana","family":"Carevic","sequence":"additional","affiliation":[{"name":"Clinical Centre of Serbia, Belgrade, Serbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liliana","family":"Preotescu","sequence":"additional","affiliation":[{"name":"Matei Bal\u015f National Institute for Infectious Diseases, Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Surbhi","family":"Malhotra-Kumar","sequence":"additional","affiliation":[{"name":"University of Antwerp, Antwerp, 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