{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T04:39:39Z","timestamp":1778647179362,"version":"3.51.4"},"reference-count":51,"publisher":"The Royal Society","issue":"168","license":[{"start":{"date-parts":[[2020,7,1]],"date-time":"2020-07-01T00:00:00Z","timestamp":1593561600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/royalsociety.org\/-\/media\/journals\/author\/Licence-to-Publish-20062019-final.pdf"},{"start":{"date-parts":[[2020,7,1]],"date-time":"2020-07-01T00:00:00Z","timestamp":1593561600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/royalsociety.org\/journals\/ethics-policies\/data-sharing-mining\/"}],"funder":[{"DOI":"10.13039\/501100000663","name":"Newnham College, University of Cambridge","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000663","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/M020193"],"award-info":[{"award-number":["BB\/M020193"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003343","name":"Cambridge Trust","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003343","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["royalsocietypublishing.org"],"crossmark-restriction":true},"short-container-title":["J. R. Soc. Interface."],"published-print":{"date-parts":[[2020,7]]},"abstract":"<jats:p>\n            Antibiotic therapy has drastically reduced the mortality and sequelae of bacterial infections. From naturally occurring to chemically synthesized, different classes of antibiotics have been successfully used without detailed knowledge of how they affect bacterial dynamics\n            <jats:italic>in vivo<\/jats:italic>\n            . However, a proportion of patients receiving antimicrobial therapy develop recrudescent infections post-treatment. Relapsing infections are attributable to incomplete clearance of bacterial populations following antibiotic administration; the metabolic profile of this antibiotic-recalcitrant bacterial subpopulation, the spatio-temporal context of its emergence and the variance of antibiotic\u2013bacterial interactions\n            <jats:italic>in vivo<\/jats:italic>\n            remain unclear. Here, we develop and apply a mechanistic mathematical model to data from a study comparing the effects of ciprofloxacin and ampicillin on the within-host dynamics of\n            <jats:italic>Salmonella enterica<\/jats:italic>\n            serovar Typhimurium in murine infections. Using the inferential capacity of our model, we show that the antibiotic-recalcitrant bacteria following ampicillin, but not ciprofloxacin, treatment belong to a non-replicating phenotype. Aligning with previous studies, we independently estimate that the lymphoid tissues and spleen are important reservoirs of non-replicating bacteria. Finally, we predict that post-treatment, the progenitors of the non-growing and growing bacterial populations replicate and die at different rates. Ultimately, the liver, spleen and mesenteric lymph nodes are all repopulated by progenitors of the previously non-growing phenotype in ampicillin-treated mice.\n          <\/jats:p>","DOI":"10.1098\/rsif.2020.0299","type":"journal-article","created":{"date-parts":[[2020,7,7]],"date-time":"2020-07-07T23:05:23Z","timestamp":1594163123000},"page":"20200299","update-policy":"https:\/\/doi.org\/10.1098\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["A data-based mathematical modelling study to quantify the effects of ciprofloxacin and ampicillin on the within-host dynamics of\n            <i>Salmonella enterica<\/i>\n            during treatment and relapse"],"prefix":"10.1098","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9659-9254","authenticated-orcid":true,"given":"Myrto","family":"Vlazaki","sequence":"first","affiliation":[{"name":"Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Omar","family":"Rossi","sequence":"additional","affiliation":[{"name":"GSK Vaccines Institute for Global Health, Via Fiorentina 1, 53100 Siena, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0076-3123","authenticated-orcid":true,"given":"David J.","family":"Price","sequence":"additional","affiliation":[{"name":"Centre of Epidemiology and Biostatistics, University of Melbourne, Grattan Street, Parkville, Victoria 3010, Australia"},{"name":"The Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Callum","family":"McLean","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew J.","family":"Grant","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pietro","family":"Mastroeni","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9158-853X","authenticated-orcid":true,"given":"Olivier","family":"Restif","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"175","published-online":{"date-parts":[[2020,7,8]]},"reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.15620\/cdc:82532"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2333"},{"key":"e_1_3_5_4_2","volume-title":"Topley and Wilson's principles of bacteriology and immunity","author":"Wilson GS","year":"1964"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.3390\/molecules181113188"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02360-18"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.06.045"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2017.09.008"},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2019.09.028"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-33264-7"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.107.1.210-216.1971"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0060074"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004857"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.28298"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2019.08.074"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.mi.47.100193.004231"},{"key":"e_1_3_5_17_2","unstructured":"Kanvatirth P Rossi O Restif O Blacklaws BA Tonks P Grant AJ Mastroeni P. 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