{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T02:53:29Z","timestamp":1790909609054,"version":"4.1.0"},"posted":{"date-parts":[[2026,9,29]]},"group-title":"Infectious Diseases (except HIV\/AIDS)","reference-count":30,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T00:00:00Z","timestamp":1790640000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"award":["K23HD099240"],"award-info":[{"award-number":["K23HD099240"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Importance<\/jats:title>\n                  <jats:p>Antibiotic-resistant infections in neonates often arise from the infant\u2019s own colonizing bacteria harboring antibiotic resistance genes (ARG). This study evaluates ARG that impact antibiotic selection and drive resistance-related mortality, termed clinically important antibiotic resistance genes (CI-ARG).<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Objective<\/jats:title>\n                  <jats:p>To determine differences in gut CI-ARG abundance in children from birth through 3 years old, stratified by neonatal intensive care unit (NICU) admission and antibiotic (abx) exposure in the first two months<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Design<\/jats:title>\n                  <jats:p>Cohort study (sequencing, analysis completed 2025-2026) using shotgun metagenomic sequencing of stool samples from infants in two studies: \u201cNeonatal Intestinal Microbiome\u201d (+NICU groups, 2015-2022), \u201cThe First 1000 Days of Life and Beyond\u201d (\u2212NICU groups, 2018-2021). Infants grouped into four cohorts: +NICU\/+abx, +NICU\/\u2212abx, \u2212NICU\/\u2212abx, and \u2212NICU\/+abx. Prespecified CI-ARG abundance compared longitudinally among groups.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Setting<\/jats:title>\n                  <jats:p>NICU, well-baby nursery, Inova Fairfax Hospital, Virginia<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Participants<\/jats:title>\n                  <jats:p>+NICU criteria: admission to the NICU, anticipated length of stay (LOS) of at least five days, maternal age \u226518 years. \u2212NICU: parents with good general health and age \u226518 years enrolled prior to infant birth. Stool samples: adequate stool processing volume, at least one stool sample from before one month and after one year of age, 7-day minimum between serial samples.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Exposures<\/jats:title>\n                  <jats:p>NICU versus well-baby nursery; antibiotics versus none in first two months of corrected age<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Main Outcomes and Measures<\/jats:title>\n                  <jats:p>Predefined primary outcome-longitudinal CI-ARG abundance by group, compared using linear mixed effects models with adjustment for multiple comparisons (Benjamini-Hochberg procedure). Predefined secondary outcomes-differences in overall microbiota and resistome composition.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>\n                    1000 serial stool samples, 179 infants (birth-39 months). Longitudinal abundance significantly differed among cohorts for 11 CI-ARG (p&lt;0.05); often higher in the +NICU groups in early life, with or without antibiotic exposure. Abundance of ARG conferring resistance to aminoglycosides, macrolides, and fluoroquinolones later decreased below \u2212NICU levels.\n                    <jats:italic>mecA<\/jats:italic>\n                    , which often drives methicillin resistance in\n                    <jats:italic>Staphylococcus<\/jats:italic>\n                    , was detected only in +NICU infants during premature period.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>This longitudinal study demonstrates significant longitudinal CI-ARG differences in children grouped by early-life NICU status and\/or antibiotic exposure. Future studies should explore the mechanisms driving these CI-ARG changes and evaluate their impact on infection risk and community spread.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Key Points<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Question<\/jats:title>\n                    <jats:p>How do clinically important antibiotic resistance genes (CI-ARG) differ longitudinally among infants up to 3 years old based on NICU admission and antibiotic exposure in the first two months of life?<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Findings<\/jats:title>\n                    <jats:p>In this cohort study of 179 infants through 39 months of age, longitudinal abundance was significantly different for 11 prespecified CI-ARG, often higher in the NICU groups in early life, with or without antibiotic exposure.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Meaning<\/jats:title>\n                    <jats:p>Children with a history of NICU hospitalization, whether due to the NICU environment itself, prematurity, or other factors, may have increased CI-ARG burden early in life, irrespective of direct antibiotic exposure.<\/jats:p>\n                  <\/jats:sec>\n                <\/jats:sec>","DOI":"10.64898\/2026.09.23.26363796","type":"posted-content","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:20:13Z","timestamp":1790727613000},"source":"Crossref","is-referenced-by-count":0,"title":["Coming Into Resistance: Clinically Important Antibiotic Resistance Genes in NICU vs. Healthy Infants"],"prefix":"10.64898","author":[{"given":"Rachel E.","family":"Strength","sequence":"first","affiliation":[{"name":"Clinical Microbiome Unit, Laboratory of Host Immunity and Microbiome, Division of Intramural Research, National Institute of Allergy and Infectious 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