{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T13:46:17Z","timestamp":1785851177138,"version":"3.56.0"},"reference-count":77,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T00:00:00Z","timestamp":1785888000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T00:00:00Z","timestamp":1785888000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"Constuction of Comprehensive Pathogen Atlas and Repository for China's Disease X for Proactive and Control","award":["2025ZD01900100, 2025ZD01900107"],"award-info":[{"award-number":["2025ZD01900100, 2025ZD01900107"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Antimicrob Agents Chemother"],"published-print":{"date-parts":[[2026,8,5]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      The global spread of antimicrobial resistance (AMR) calls for advanced surveillance frameworks capable of tracking high-risk resistance genes across genomic, temporal, and ecological environments. To address this, we designed an integrated genomic epidemiology workflow, encompassing antibiotic resistance gene sequence alignment and phylogenetic classification, integration of whole-genome functional annotation, and individual analysis of key bacterial strains. Applying this framework, we obtained 1,026 chloramphenicol-florfenicol resistance (\n                      <jats:italic toggle=\"yes\">cfr<\/jats:italic>\n                      )-like sequences through homology searches, and phylogenetic analysis resolved them into 11 monophyletic clusters, including the newly identified\n                      <jats:italic toggle=\"yes\">cfr<\/jats:italic>\n                      (F) and\n                      <jats:italic toggle=\"yes\">cfr<\/jats:italic>\n                      (G) variants. From the screening of 702,252 bacterial genomes, we identified 5,901\n                      <jats:italic toggle=\"yes\">cfr<\/jats:italic>\n                      -positive isolates comprising 11 distinct\n                      <jats:italic toggle=\"yes\">cfr<\/jats:italic>\n                      variants. The earliest variant,\n                      <jats:italic toggle=\"yes\">cfr<\/jats:italic>\n                      (G), was detected in a soil isolate dating to 1893. Genomic localization analysis revealed that\n                      <jats:italic toggle=\"yes\">clbA<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">clbC<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">cfr<\/jats:italic>\n                      (E),\n                      <jats:italic toggle=\"yes\">cfr<\/jats:italic>\n                      (F), and\n                      <jats:italic toggle=\"yes\">cfr<\/jats:italic>\n                      (C) were putatively predominantly chromosomal, whereas\n                      <jats:italic toggle=\"yes\">cfr<\/jats:italic>\n                      (G),\n                      <jats:italic toggle=\"yes\">cfr<\/jats:italic>\n                      (B),\n                      <jats:italic toggle=\"yes\">cipA<\/jats:italic>\n                      , and\n                      <jats:italic toggle=\"yes\">clbB<\/jats:italic>\n                      were putatively mainly plasmid-borne. Importantly,\n                      <jats:italic toggle=\"yes\">cfr-<\/jats:italic>\n                      like genes frequently co-localize with other last-resort antibiotic resistance genes (ARGs), including\n                      <jats:italic toggle=\"yes\">vanA<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">optrA<\/jats:italic>\n                      , and carbapenemase genes, on the same isolate, promoting multidrug resistance. Beyond gene detection, this study clarifies the context-dependent transmission risks of resistance determinants and provides a strategic framework for anticipating resistance convergence and informing preemptive AMR surveillance.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/aac.00122-26","type":"journal-article","created":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T14:59:12Z","timestamp":1783695552000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["A genomic framework for tracking antibiotic resistance genes: global dissemination of\n                    <i>cfr<\/i>\n                    -family 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