{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:23:55Z","timestamp":1787009035019,"version":"build-2736575974"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100022963","name":"\u2018Leading Goose\u2019 R&D Program of Zhejiang Province","doi-asserted-by":"publisher","award":["2023C03045"],"award-info":[{"award-number":["2023C03045"]}],"id":[{"id":"10.13039\/100022963","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004731","name":"Zhejiang Provincial Natural Science Foundation of China","doi-asserted-by":"publisher","award":["LY23C180001"],"award-info":[{"award-number":["LY23C180001"]}],"id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hangzhou Institute for Advanced Study"},{"DOI":"10.13039\/501100015361","name":"UCAS","doi-asserted-by":"publisher","award":["2023HIAS-Y031"],"award-info":[{"award-number":["2023HIAS-Y031"]}],"id":[{"id":"10.13039\/501100015361","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The genus Bordetella comprises Gram-negative pathogens, notably B. pertussis, which causes whooping cough, underscoring the need to characterize antimicrobial resistance (AMR) within this group. However, reports of acquired antimicrobial resistance genes (ARGs) in non-B. pertussis Bordetella species remain scarce.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Non\u2013B. pertussis Bordetella genomes were retrieved from NCBI, adapters trimmed and low-quality reads filtered, then assembled for analysis. ARGs were identified with Abricate, ResFinder, and BLAST, and their genomic contexts visualized using Easyfig. Core-genome SNP phylogeny and Bayesian clustering delineated lineages, and SNP-based thresholds quantified transmission.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Across 746 genomes, 105 ARGs were identified in three non-B. pertussis species: B. bronchiseptica (96 ARGs), B. trematum (7 ARGs) and B. avium (2 ARGs). Ten distinct ARG types covering sulphonamide (sul1, sul2), tetracycline (tet(A), tet(G), tet(31)), aminoglycoside (aac(6\u2032)-IIa, aadA2, aph(3\u2033)-Ib, aph(6)-Id) and \u03b2-lactam (blaOXA-2) resistance were observed. Core-genome SNP analysis of 238 B. bronchiseptica strains resolved three lineages, of which lineage\u202f2 harboured the greatest diversity of multidrug-resistant isolates. Transmission-event quantification using SNP thresholds revealed frequent international and cross-host spread, notably human-dog\/rabbit transfers and international dissemination between France and the United States.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>These findings underscore the importance of monitoring AMR in Bordetella species to anticipate and mitigate the spread of resistant strains.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/jac\/dkaf418","type":"journal-article","created":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T12:00:04Z","timestamp":1761134404000},"source":"Crossref","is-referenced-by-count":3,"title":["Acquired antimicrobial resistance genes in\n                    <i>Bordetella<\/i>\n                    Species: a global genomic analysis"],"prefix":"10.1093","volume":"81","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3605-4022","authenticated-orcid":false,"given":"Biao","family":"Tang","sequence":"first","affiliation":[{"name":"Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, Hangzhou, University of Chinese Academy of Sciences ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaohe","family":"Hu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, Hangzhou, University of Chinese Academy of Sciences ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Song","sequence":"additional","affiliation":[{"name":"Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, Hangzhou, University of Chinese Academy of Sciences ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xu","family":"Liu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, Hangzhou, University of Chinese Academy of Sciences ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guoping","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, Hangzhou, University of Chinese Academy of Sciences ,","place":["China"]},{"name":"National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai ,","place":["China"]},{"name":"Department of Microbiology, School 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