{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T06:03:42Z","timestamp":1777529022040,"version":"3.51.4"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T00:00:00Z","timestamp":1758672000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01AI108695-01A"],"award-info":[{"award-number":["R01AI108695-01A"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["KL2TR002545"],"award-info":[{"award-number":["KL2TR002545"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["U19AI110818"],"award-info":[{"award-number":["U19AI110818"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["5T32ES012870"],"award-info":[{"award-number":["5T32ES012870"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006939","name":"Emory University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006939","id-type":"DOI","asserted-by":"publisher"}]},{"name":"MP3 Initiative"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,12,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The effects of antibiotic use on children\u2019s gut microbiomes and resistomes are not well characterized in middle-income countries, where antibiotic consumption is exceptionally common.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>We characterized the effects of antibiotics commonly used by Peruvian children (i.e. amoxicillin, azithromycin, cefalexin, trimethoprim\/sulfamethoxazole) on the \u03b1-diversity, \u03b2-diversity and abundance of gut genera and antibiotic resistance genes (ARGs) from 3 to 16\u2005months.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>This study included 54 children from a prospective cohort of enteric infections in peri-urban Lima, 2016\u201319. Stools collected at 3, 6, 7, 9, 12 and 16\u2005months underwent DNA extraction and short-read metagenomic sequencing. We profiled the taxonomy of stool metagenomes and assessed ARG abundance by aligning reads to the ResFinder database. We used daily surveillance data (40\u200a662 observations) to tabulate the number of antibiotic courses consumed in the 30\u2005days prior to stool sampling. Using linear mixed models, we examined associations of recent antibiotic use with richness, diversity and abundance of gut genera and ARGs over time.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Each additional recent antibiotic course decreased Bifidobacterium and Dialister abundance and increased Veillonella abundance, although gut richness and diversity were not affected. Recent use of amoxicillin, azithromycin, cefalexin or trimethoprim\/sulfamethoxazole, specifically, did not impact gut microbiome measures. Amoxicillin, azithromycin and trimethoprim\/sulfamethoxazole significantly enriched multiple ARGs and amoxicillin use significantly increased total ARGs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Common antibiotics like amoxicillin and azithromycin appear to be key drivers of the paediatric gut resistome. Resistome perturbations appeared to be stronger, or persist for longer, than gut microbiome effects in this middle-income country setting.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/jac\/dkaf358","type":"journal-article","created":{"date-parts":[[2025,9,9]],"date-time":"2025-09-09T11:35:19Z","timestamp":1757417719000},"page":"3248-3256","source":"Crossref","is-referenced-by-count":1,"title":["Effects of commonly used antibiotics on children\u2019s developing gut microbiomes and resistomes in peri-urban Lima, Peru"],"prefix":"10.1093","volume":"80","author":[{"given":"Neha","family":"Sehgal","sequence":"first","affiliation":[{"name":"Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University , Atlanta, GA ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monica J","family":"Pajuelo","sequence":"additional","affiliation":[{"name":"Laboratorio de Microbiolog\u00eda Molecular, Laboratorios de Investigaci\u00f3n y Desarrollo, Facultad de Ciencias e Ingenier\u00eda, Universidad Peruana Cayetano Heredia , Lima ,","place":["Peru"]},{"name":"Department of International Health, Johns Hopkins Bloomberg School of Public Health , Baltimore, MD ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert H","family":"Gilman","sequence":"additional","affiliation":[{"name":"Laboratorio de Microbiolog\u00eda Molecular, Laboratorios de Investigaci\u00f3n y Desarrollo, Facultad de Ciencias e Ingenier\u00eda, Universidad Peruana Cayetano Heredia , Lima ,","place":["Peru"]},{"name":"Department of International Health, Johns Hopkins Bloomberg School of Public Health , Baltimore, MD ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amy J","family":"Pickering","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering, University of California, Berkeley , Berkeley, CA ,","place":["USA"]},{"name":"Blum Center for Developing Economies, University of California, Berkeley , Berkeley, CA ,","place":["USA"]},{"name":"Chan Zuckerberg Biohub , San Francisco, CA ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ashlee M","family":"Earl","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard , Cambridge, MA ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9132-7249","authenticated-orcid":false,"given":"Colin J","family":"Worby","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard , Cambridge, MA ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6526-116X","authenticated-orcid":false,"given":"Maya 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