{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T01:14:19Z","timestamp":1779153259521,"version":"3.51.4"},"reference-count":30,"publisher":"SAGE Publications","license":[{"start":{"date-parts":[[2025,6,5]],"date-time":"2025-06-05T00:00:00Z","timestamp":1749081600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,6,5]],"date-time":"2025-06-05T00:00:00Z","timestamp":1749081600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"funder":[{"DOI":"10.13039\/501100020021","name":"Avant Foundation","doi-asserted-by":"publisher","award":["Doctor-in-Training Research Scholarship"],"award-info":[{"award-number":["Doctor-in-Training Research Scholarship"]}],"id":[{"id":"10.13039\/501100020021","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001077","name":"Royal Brisbane and Women\u2019s Hospital Foundation","doi-asserted-by":"publisher","award":["Research Grant"],"award-info":[{"award-number":["Research Grant"]}],"id":[{"id":"10.13039\/501100001077","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017511","name":"Metro North Hospital and Health Service","doi-asserted-by":"publisher","award":["Queensland Health Junior Doctor Research Fellowshi"],"award-info":[{"award-number":["Queensland Health Junior Doctor Research Fellowshi"]}],"id":[{"id":"10.13039\/100017511","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["Therapeutic Advances in Infection"],"published-print":{"date-parts":[[2025,7]]},"abstract":"<jats:sec>\n                    <jats:title>Background:<\/jats:title>\n                    <jats:p>Understanding how the gut microbiome adapts on exposure to individual antibiotics, with respect to antimicrobial resistance gene (ARG) enrichment, is important.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objectives:<\/jats:title>\n                    <jats:p>To characterise the changes that occur in the gut microbiome of patients enrolled in an antibiotic clinical trial and to propose methods in which to embed gut microbiome analysis into clinical trials.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Design:<\/jats:title>\n                    <jats:p>This was a prospective cohort study of hospitalised patients who were successfully enrolled and randomised into two clinical trials between January 2021 to December 2021.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods:<\/jats:title>\n                    <jats:p>Adult patients admitted to the hospital with a bloodstream infection have been randomised to receive either benzylpenicillin, ampicillin, cefazolin, ceftriaxone, piperacillin-tazobactam or meropenem at a single institution. Faecal specimens were collected at enrolment and every second day until discharge. Each specimen underwent DNA sequencing to determine microbial diversity and ARG abundance.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results:<\/jats:title>\n                    <jats:p>\n                      Ten patients (including six females) were included. DNA concentration and sampling quality were markedly lower for rectal swabs compared to stool samples. Relative abundance of\n                      <jats:italic toggle=\"yes\">Enterococcus faecium<\/jats:italic>\n                      was increased in individual patients where treatment included ampicillin, meropenem and piperacillin-tazobactam. Piperacillin-tazobactam also increased the abundance of key beta-lactamase genes (\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>SHV-100<\/jats:sub>\n                      ,\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>OXA-392<\/jats:sub>\n                      ,\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>CMY-18<\/jats:sub>\n                      ). Ampicillin increased the abundance of\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>TEM-1A<\/jats:sub>\n                      . There were no extended-spectrum beta-lactamase (ESBL) or carbapenemase genes detected in our study. The presence of key anaerobes such as\n                      <jats:italic toggle=\"yes\">Clostridium<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">Bifidobacterium<\/jats:italic>\n                      species appeared to play an important role in colonisation resistance of\n                      <jats:italic toggle=\"yes\">E. faecium<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">Clostridioides difficile<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion:<\/jats:title>\n                    <jats:p>Differential changes in anaerobic bacterial genera on exposure to antibiotics may be a key determinant of colonisation resistance. The pre-analytical phase of microbiome analysis is a critical factor in data quality and interpretation.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1177\/20499361251337597","type":"journal-article","created":{"date-parts":[[2025,6,5]],"date-time":"2025-06-05T08:05:24Z","timestamp":1749110724000},"update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":1,"title":["Differences in antimicrobial resistance gene abundance and microbial diversity of the gut microbiome in patients on antibiotics enrolled in a clinical trial"],"prefix":"10.1177","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7262-7529","authenticated-orcid":false,"given":"Adam G.","family":"Stewart","sequence":"first","affiliation":[{"name":"Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women\u2019s Hospital Campus, Brisbane, QLD, Australia"},{"name":"Central Microbiology, Pathology Queensland, Royal Brisbane and Women\u2019s Hospital, Brisbane, QLD, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick N. A.","family":"Harris","sequence":"additional","affiliation":[{"name":"Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women\u2019s Hospital Campus, Brisbane, QLD, Australia"},{"name":"Central Microbiology, Pathology Queensland, Royal Brisbane and Women\u2019s Hospital, Brisbane, QLD, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rikki M. A.","family":"Graham","sequence":"additional","affiliation":[{"name":"Q-PHIRE Genomics and Public Health Microbiology, Queensland Health Forensic and Scientific Services, Coopers Plains, Brisbane, QLD, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amy V.","family":"Jennison","sequence":"additional","affiliation":[{"name":"Q-PHIRE Genomics and Public Health Microbiology, Queensland Health Forensic and Scientific Services, Coopers Plains, Brisbane, QLD, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sanmarie","family":"Schlebusch","sequence":"additional","affiliation":[{"name":"Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women\u2019s Hospital Campus, Brisbane, QLD, Australia"},{"name":"Central Microbiology, Pathology Queensland, Royal Brisbane and Women\u2019s Hospital, Brisbane, QLD, Australia"},{"name":"Q-PHIRE Genomics and Public Health Microbiology, Queensland Health Forensic and Scientific Services, Coopers Plains, Brisbane, QLD, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Asha","family":"Kakkanat","sequence":"additional","affiliation":[{"name":"Q-PHIRE Genomics and Public Health Microbiology, Queensland Health Forensic and Scientific Services, Coopers Plains, Brisbane, QLD, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tiffany","family":"Harris-Brown","sequence":"additional","affiliation":[{"name":"Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women\u2019s Hospital Campus, Brisbane, QLD, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David L.","family":"Paterson","sequence":"additional","affiliation":[{"name":"Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women\u2019s Hospital Campus, Brisbane, QLD, Australia"},{"name":"ADVANCE-ID, Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brian M.","family":"Forde","sequence":"additional","affiliation":[{"name":"Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women\u2019s Hospital Campus, Brisbane, QLD, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"179","published-online":{"date-parts":[[2025,6,5]]},"reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(21)02724-0"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-023-00933-y"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03986-2"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2022.110649"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1002\/mbo3.1260"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41385-018-0053-0"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-018-0029-9"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa1877"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-022-02487-0"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0176469"},{"issue":"1","key":"e_1_3_4_13_2","first-page":"000748","article-title":"ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes","volume":"8","author":"Florensa AF","year":"2022","unstructured":"Florensa AF, Sommer Kaas R, Thomas Lanken Conradsen Clausen P, et al. 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