{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T04:38:15Z","timestamp":1778128695032,"version":"3.51.4"},"reference-count":35,"publisher":"American Society for Microbiology","issue":"10","license":[{"start":{"date-parts":[[2015,10,1]],"date-time":"2015-10-01T00:00:00Z","timestamp":1443657600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Antimicrob Agents Chemother"],"published-print":{"date-parts":[[2015,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            To gain insights into the diversification trajectories of\n            <jats:italic>qnrB<\/jats:italic>\n            genes, a phylogenetic and comparative genomics analysis of these genes and their surrounding genetic sequences was performed. For this purpose,\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Citrobacter<\/jats:named-content>\n            sp. isolates (\n            <jats:italic>n<\/jats:italic>\n            = 21) and genome or plasmid sequences (\n            <jats:italic>n<\/jats:italic>\n            = 56) available in public databases harboring complete or truncated\n            <jats:italic>qnrB<\/jats:italic>\n            genes were analyzed.\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Citrobacter<\/jats:named-content>\n            species identification was performed by phylogenetic analysis of different genotypic markers. The clonal relatedness among isolates, the location of\n            <jats:italic>qnrB<\/jats:italic>\n            genes, and the genetic surroundings of\n            <jats:italic>qnrB<\/jats:italic>\n            genes were investigated by pulsed-field gel electrophoresis (PFGE), S1-\/I-CeuI-PFGE and hybridization, and PCR mapping and sequencing, respectively. Identification of\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Citrobacter<\/jats:named-content>\n            isolates was achieved using\n            <jats:italic>leuS<\/jats:italic>\n            and\n            <jats:italic>recN<\/jats:italic>\n            gene sequences, and isolates characterized in this study were diverse and harbored chromosomal\n            <jats:italic>qnrB<\/jats:italic>\n            genes. Phylogenetic analysis of all known\n            <jats:italic>qnrB<\/jats:italic>\n            genes revealed seven main clusters and two branches, with most of them included in two clusters. Specific platforms (comprising\n            <jats:italic>pspF<\/jats:italic>\n            and\n            <jats:italic>sapA<\/jats:italic>\n            and varying in synteny and\/or identity of other genes and intergenic regions) were associated with each one of these\n            <jats:italic>qnrB<\/jats:italic>\n            clusters, and the reliable identification of all\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Citrobacter<\/jats:named-content>\n            isolates revealed that each platform evolved in different recognizable (\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Citrobacter freundii<\/jats:named-content>\n            ,\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">C. braakii<\/jats:named-content>\n            ,\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">C. werkmanii<\/jats:named-content>\n            , and\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">C. pasteurii<\/jats:named-content>\n            ) and putatively new species. A high identity was observed between some of the platforms identified in the chromosome of\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Citrobacter<\/jats:named-content>\n            spp. and in different plasmids of\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Enterobacteriaceae<\/jats:named-content>\n            . Our data corroborate\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Citrobacter<\/jats:named-content>\n            as the origin of\n            <jats:italic>qnrB<\/jats:italic>\n            and further suggest divergent evolution of closely related\n            <jats:italic>qnrB<\/jats:italic>\n            genes\/platforms in particular\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Citrobacter<\/jats:named-content>\n            spp., which were delineated using particular genotypic markers.\n          <\/jats:p>","DOI":"10.1128\/aac.00027-15","type":"journal-article","created":{"date-parts":[[2015,7,14]],"date-time":"2015-07-14T02:24:44Z","timestamp":1436840684000},"page":"5951-5958","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":44,"title":["Phylogeny and Comparative Genomics Unveil Independent Diversification Trajectories of\n            <i>qnrB<\/i>\n            and Genetic Platforms within Particular Citrobacter Species"],"prefix":"10.1128","volume":"59","author":[{"given":"Teresa G.","family":"Ribeiro","sequence":"first","affiliation":[{"name":"UCIBIO\/REQUIMTE, Laborat\u00f3rio de Microbiologia, Faculdade de Farm\u00e1cia, Universidade do Porto, Porto, Portugal"}]},{"given":"\u00c2ngela","family":"Novais","sequence":"additional","affiliation":[{"name":"UCIBIO\/REQUIMTE, Laborat\u00f3rio de Microbiologia, Faculdade de Farm\u00e1cia, Universidade do Porto, Porto, Portugal"}]},{"given":"Raquel","family":"Branquinho","sequence":"additional","affiliation":[{"name":"UCIBIO\/REQUIMTE, Laborat\u00f3rio de Microbiologia, Faculdade de Farm\u00e1cia, Universidade do Porto, Porto, Portugal"}]},{"given":"Elisabete","family":"Machado","sequence":"additional","affiliation":[{"name":"UCIBIO\/REQUIMTE, Laborat\u00f3rio de Microbiologia, Faculdade de Farm\u00e1cia, Universidade do Porto, Porto, Portugal"},{"name":"FP-ENAS\/CEBIMED, Faculdade de Ci\u00eancias da Sa\u00fade, Universidade Fernando Pessoa, Porto, Portugal"}]},{"given":"Lu\u00edsa","family":"Peixe","sequence":"additional","affiliation":[{"name":"UCIBIO\/REQUIMTE, Laborat\u00f3rio de Microbiologia, Faculdade de Farm\u00e1cia, Universidade do Porto, Porto, Portugal"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00239-008-9131-3"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00016-09"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.05187-11"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02396-12"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01042-07"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijs.0.000122"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.33.1.242-245.1995"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.47.1.268-273.2003"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijfoodmicro.2013.08.005"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msr121"},{"key":"e_1_3_3_12_2","first-page":"406","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"Saitou N","year":"1987","unstructured":"Saitou N, Nei M. 1987. 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