{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T10:47:06Z","timestamp":1788432426014,"version":"build-2803163510"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2025,10,3]],"date-time":"2025-10-03T00:00:00Z","timestamp":1759449600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Australian National Health and Medical Research Council","award":["GNT1194978"],"award-info":[{"award-number":["GNT1194978"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,12,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The origins of several antibiotic resistance genes have been traced to intrinsic genes present in bacterial chromosomes. The aphA1 gene, which confers resistance to the aminoglycosides kanamycin and neomycin, is commonly found in diverse Gram-negative bacterial pathogens, and is associated with several different mobile genetic elements. However, its origin had not been identified.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>To determine whether the aphA1-containing segments in novel compound and pseudo-compound transposons found in three historic plasmids, pIE545, R478 and Rts1, are found in the chromosome of a specific bacterial species.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Passenger segments of transposons containing the aphA1 gene were compared to one another and to chromosomal sequences in GenBank using BLAST.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In pIE545, aphA1 is in a 5424\u2005bp compound transposon, TnaphA1-pIE545, that is bounded by directly oriented copies of IS102. The 3.3\u2005kb aphA1-containing passenger segment is &amp;gt;99% identical to a contiguous part of several Klebsiella michiganensis chromosomes. The 4.3\u2005kb aphA1-containing segment of the IS26-bounded pseudo-compound transposon PTnaphA1-R478 in R478 is also &amp;gt;99% identical to a contiguous part of several K. michiganensis chromosomes that differ in the gene content surrounding aphA1. The 2.2\u2005kb passenger segment of the IS26-bounded PTn2680 from Rts1 arose via a third independent acquisition from a K. michiganensis chromosome.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>The aphA1 gene has been captured and mobilized on at least three occasions from K. michiganensis chromosomes with related but distinct surrounding configurations.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/jac\/dkaf372","type":"journal-article","created":{"date-parts":[[2025,9,17]],"date-time":"2025-09-17T12:02:08Z","timestamp":1758110528000},"page":"3340-3344","source":"Crossref","is-referenced-by-count":3,"title":["The\n                    <i>aphA1<\/i>\n                    kanamycin and neomycin resistance gene originated in\n                    <i>Klebsiella michiganensis<\/i>"],"prefix":"10.1093","volume":"80","author":[{"given":"Robert A","family":"Moran","sequence":"first","affiliation":[{"name":"School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2062-3312","authenticated-orcid":false,"given":"Ruth M","family":"Hall","sequence":"additional","affiliation":[{"name":"School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,10,3]]},"reference":[{"key":"2025120206223945600_dkaf372-B1","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1016\/S0147-619X(02)00017-3","article-title":"Chromosomal sequences from Klebsiella pneumoniae flank the SHV-5 extended-spectrum beta-lactamase gene in pACM1","volume":"48","author":"Preston","year":"2002","journal-title":"Plasmid"},{"key":"2025120206223945600_dkaf372-B2","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1093\/jac\/dkh251","article-title":"Evolutionary mapping of the SHV beta-lactamase and evidence for two separate IS26-dependent blaSHV mobilization events from the Klebsiella pneumoniae chromosome","volume":"54","author":"Ford","year":"2004","journal-title":"J Antimicrob Chemother"},{"key":"2025120206223945600_dkaf372-B3","doi-asserted-by":"publisher","first-page":"820","DOI":"10.1111\/j.1574-6976.2011.00277.x","article-title":"Analysis of antibiotic resistance regions in Gram-negative bacteria","volume":"35","author":"Partridge","year":"2011","journal-title":"FEMS Microbiol Rev"},{"key":"2025120206223945600_dkaf372-B4","doi-asserted-by":"publisher","first-page":"e0011922","DOI":"10.1128\/mmbr.00119-22","article-title":"IS26 and the IS26 family: versatile resistance gene movers and genome reorganizers","volume":"88","author":"Harmer","year":"2024","journal-title":"Microbiol Mol Biol Rev"},{"key":"2025120206223945600_dkaf372-B5","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1038\/s42003-020-01545-5","article-title":"A framework for identifying the recent origins of mobile antibiotic resistance genes","volume":"4","author":"Ebmeyer","year":"2021","journal-title":"Commun Biol"},{"key":"2025120206223945600_dkaf372-B6","doi-asserted-by":"publisher","first-page":"2039","DOI":"10.1111\/j.1365-2958.1991.tb00826.x","article-title":"Evolved neomycin phosphotransferase from an isolate of Klebsiella pneumoniae","volume":"5","author":"Lee","year":"1991","journal-title":"Mol Microbiol"},{"key":"2025120206223945600_dkaf372-B7","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/j.plasmid.2017.05.004","article-title":"pIP40a, a type 1 IncC plasmid from 1969 carries the integrative element GIsul2 and a novel class II mercury resistance transposon","volume":"92","author":"Harmer","year":"2017","journal-title":"Plasmid"},{"key":"2025120206223945600_dkaf372-B8","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1016\/j.plasmid.2019.02.005","article-title":"Analysis of two B\/O plasmids, R805a from 1972 and pCERC6 from 2008, reveals extensive mosaicism in B\/O plasmid backbones","volume":"102","author":"Moran","year":"2019","journal-title":"Plasmid"},{"key":"2025120206223945600_dkaf372-B9","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1128\/jb.163.1.55-60.1985","article-title":"Organization of the Tn6-related kanamycin resistance transposon Tn2680 carrying two copies of IS26 and an IS903 variant, IS903B","volume":"163","author":"Mollet","year":"1985","journal-title":"J Bacteriol"},{"key":"2025120206223945600_dkaf372-B10","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1016\/j.plasmid.2018.08.001","article-title":"Evolution and typing of IncC plasmids contributing to antibiotic resistance in Gram-negative bacteria","volume":"99","author":"Ambrose","year":"2018","journal-title":"Plasmid"},{"key":"2025120206223945600_dkaf372-B11","doi-asserted-by":"publisher","first-page":"102528","DOI":"10.1016\/j.plasmid.2020.102528","article-title":"Evolution and dissemination of L and M plasmid lineages carrying antibiotic resistance genes in diverse Gram-negative bacteria","volume":"113","author":"Blackwell","year":"2021","journal-title":"Plasmid"},{"key":"2025120206223945600_dkaf372-B12","doi-asserted-by":"publisher","first-page":"2667","DOI":"10.1128\/AAC.01407-08","article-title":"Abar5, a large multiple-antibiotic resistance region found in Acinetobacter baumannii","volume":"53","author":"Post","year":"2009","journal-title":"Antimicrob Agents Chemother"},{"key":"2025120206223945600_dkaf372-B13","doi-asserted-by":"publisher","first-page":"1504","DOI":"10.1093\/jac\/dkr163","article-title":"Aminoglycoside resistance in multiply antibiotic-resistant Acinetobacter baumannii belonging to global clone 2 from Australian hospitals","volume":"66","author":"Nigro","year":"2011","journal-title":"J Antimicrob Chemother"},{"key":"2025120206223945600_dkaf372-B14","doi-asserted-by":"publisher","first-page":"1031","DOI":"10.1093\/jac\/dkw542","article-title":"Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore","volume":"72","author":"Blackwell","year":"2017","journal-title":"J Antimicrob Chemother"},{"key":"2025120206223945600_dkaf372-B15","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1016\/0022-2836(81)90438-1","article-title":"Nucleotide sequence of the kanamycin resistance transposon Tn903","volume":"147","author":"Oka","year":"1981","journal-title":"J Mol Biol"},{"key":"2025120206223945600_dkaf372-B16","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1016\/0147-619x(87)90028-x","article-title":"Tn602: a naturally occurring relative of Tn903 with direct repeats","volume":"17","author":"Stibitz","year":"1987","journal-title":"Plasmid"},{"key":"2025120206223945600_dkaf372-B17","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1016\/0147-619X(87)90006-0","article-title":"A pathway for the evolution of the plasmid NTP16 involving the novel kanamycin resistance transposon Tn4352","volume":"17","author":"Wrighton","year":"1987","journal-title":"Plasmid"},{"key":"2025120206223945600_dkaf372-B18","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1002\/jobm.19830230610","article-title":"Characterization of conjugative plasmids belonging to a new incompatibility group (IncZ)","volume":"23","author":"Tsch\u00e4pe","year":"1983","journal-title":"Z Allg Mikrobiol"},{"key":"2025120206223945600_dkaf372-B19","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J Comput Biol"},{"key":"2025120206223945600_dkaf372-B20","doi-asserted-by":"publisher","first-page":"D32","DOI":"10.1093\/nar\/gkj014","article-title":"ISfinder: the reference centre for bacterial insertion sequences","volume":"34","author":"Siguier","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2025120206223945600_dkaf372-B21","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2025120206223945600_dkaf372-B22","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1186\/s13568-023-01618-8","article-title":"Klebsiella michiganensis: a nitrogen-fixing endohyphal bacterium from Ustilago maydis","volume":"13","author":"Liang","year":"2023","journal-title":"AMB Express"},{"key":"2025120206223945600_dkaf372-B23","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1089\/mdr.2011.0037","article-title":"Transposon Tn5393e carrying the aphA1-containing transposon Tn6023 upstream of strAB does not confer resistance to streptomycin","volume":"17","author":"Cain","year":"2011","journal-title":"Microb Drug Resist"},{"key":"2025120206223945600_dkaf372-B24","doi-asserted-by":"publisher","first-page":"1121","DOI":"10.1093\/jac\/dks004","article-title":"Evolution of IncHI2 plasmids via acquisition of transposons carrying antibiotic resistance determinants","volume":"67","author":"Cain","year":"2012","journal-title":"J Antimicrob Chemother"},{"key":"2025120206223945600_dkaf372-B25","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1016\/j.plasmid.2004.06.006","article-title":"The complete nucleotide sequence of the resistance plasmid R478: defining the backbone components of incompatibility group H conjugative plasmids through comparative genomics","volume":"52","author":"Gilmour","year":"2004","journal-title":"Plasmid"},{"key":"2025120206223945600_dkaf372-B26","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1007\/BF00260701","article-title":"Inter- and intramolecular transposition of Tn903","volume":"227","author":"Bernardi","year":"1991","journal-title":"Mol Gen Genet"},{"key":"2025120206223945600_dkaf372-B27","doi-asserted-by":"publisher","first-page":"2874","DOI":"10.1093\/jac\/dkaf227","article-title":"The catA1 chloramphenicol resistance gene originated in Atlantibacter hermannii","volume":"80","author":"Moran","year":"2025","journal-title":"J Antimicrob Chemother"}],"container-title":["Journal of Antimicrobial Chemotherapy"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jac\/article-pdf\/80\/12\/3340\/64480887\/dkaf372.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jac\/article-pdf\/80\/12\/3340\/64480887\/dkaf372.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T11:22:41Z","timestamp":1764674561000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jac\/article\/80\/12\/3340\/8271846"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,3]]},"references-count":27,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2025,10,3]]},"published-print":{"date-parts":[[2025,12,2]]}},"URL":"https:\/\/doi.org\/10.1093\/jac\/dkaf372","relation":{},"ISSN":["0305-7453","1460-2091"],"issn-type":[{"value":"0305-7453","type":"print"},{"value":"1460-2091","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,12]]},"published":{"date-parts":[[2025,10,3]]}}}