{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T13:21:30Z","timestamp":1787836890009,"version":"build-2784847793"},"reference-count":47,"publisher":"American Veterinary Medical Association (AVMA)","license":[{"start":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T00:00:00Z","timestamp":1787788800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["ajvr"],"published-print":{"date-parts":[[2026,8,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec id=\"sc_a1\">\n                    <jats:title>Objective<\/jats:title>\n                    <jats:p>To utilize full-length 16S rRNA long-read sequencing to (1) describe the microbiome profile of synovial fluid, previously classified by cytology and microbial culture, from foals with and without septic arthritis and (2) determine the agreement between the microbiome profiles and microbial culture.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sc_a2\">\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>A retrospective observational study was conducted using synovial samples collected from foals treated at a single equine referral center (from 2018 through 2024). The synovial fluid was classified as septic or not septic using standard cytological and microbial culture methods. Deoxyribonucleic acid was extracted from stored samples and sequenced using a MinION sequencer. Linear mixed modeling was used to determine the relationships between \u03b1 diversity and age, affected joint, and cytological and culture status. \u03b2 diversity was assessed using permutational multivariate ANOVA. Differential taxa were identified with ALDEx2. The agreement between sequencing and culture was evaluated using the Gwet coefficient.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sc_a3\">\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Fifty samples met inclusion criteria. \u03b1 diversity (Shannon index) was higher in culture-positive samples (mean difference, 0.42; 95% CI, 0.12, 0.72). Microbiome composition differed by culture (\n                      <jats:italic>R<\/jats:italic>\n                      <jats:sup>2<\/jats:sup>\n                      for Aitchison dissimilarity distance, 0.091) and cytology status (\n                      <jats:italic>R<\/jats:italic>\n                      <jats:sup>2<\/jats:sup>\n                      for Jaccard dissimilarity distance, 0.029). No taxa differed by age, joint, or cytology.\n                      <jats:italic>Klebsiella<\/jats:italic>\n                      were significantly more abundant in culture-positive samples (ALDEx2 standardized effect size, 0.65; 95% CI, \u22121.63, 7.01). Agreement between positive culture and the predominant sequenced genus was 0.774 (Gwet AC\n                      <jats:sub>1<\/jats:sub>\n                      coefficient) with a probabilistic benchmark interval of 0.6 to 0.8 (substantial agreement).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sc_a4\">\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Next-generation sequencing and culture results were substantially aligned.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sc_a5\">\n                    <jats:title>Clinical Relevance<\/jats:title>\n                    <jats:p>Next-generation sequencing may aid diagnosis in suspected septic arthritis cases with negative culture results.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.2460\/ajvr.26.03.0145","type":"journal-article","created":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T12:53:30Z","timestamp":1787835210000},"page":"1-10","source":"Crossref","is-referenced-by-count":0,"title":["Full-length 16S ribosomal RNA sequencing of foal synovial fluid shows substantial agreement with microbial culture"],"prefix":"10.2460","author":[{"given":"Hannah","family":"Chenail","sequence":"first","affiliation":[{"name":"Rood & Riddle Equine Hospital, Lexington, KY"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas D.","family":"Hacker","sequence":"additional","affiliation":[{"name":"VERO Program, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Canyon, TX"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brett","family":"Woodie","sequence":"additional","affiliation":[{"name":"Rood & Riddle Equine Hospital, Lexington, KY"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew A.","family":"Scott","sequence":"additional","affiliation":[{"name":"VERO Program, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Canyon, TX"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul S.","family":"Morley","sequence":"additional","affiliation":[{"name":"VERO Program, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Canyon, TX"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma","family":"Adam","sequence":"additional","affiliation":[{"name":"Gluck Equine Research Center, University of Kentucky, Lexington, KY"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6023-9230","authenticated-orcid":true,"given":"Allen E.","family":"Page","sequence":"additional","affiliation":[{"name":"Gluck Equine Research Center, University of Kentucky, Lexington, KY"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Valeris-Chacin","sequence":"additional","affiliation":[{"name":"VERO Program, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Canyon, TX"},{"name":"Contributed equally to this work."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolyn","family":"Arnold","sequence":"additional","affiliation":[{"name":"School of Veterinary Medicine, Texas Tech University, Amarillo, TX"},{"name":"Contributed equally to this work."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1272","reference":[{"issue":"2","key":"B1","series-title":"Ir Vet J","first-page":"102","article-title":"Analysis of factors influencing prognosis in foals with septic arthritis","volume":"61","author":"Vos NJ","year":"2008","unstructured":"Vos NJ, Ducharme NG. 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