{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T09:41:11Z","timestamp":1790674871191,"version":"4.1.0"},"reference-count":109,"publisher":"American Society for Microbiology","issue":"1","license":[{"start":{"date-parts":[[2022,2,22]],"date-time":"2022-02-22T00:00:00Z","timestamp":1645488000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2022,2,22]],"date-time":"2022-02-22T00:00:00Z","timestamp":1645488000000},"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":["mSystems"],"published-print":{"date-parts":[[2022,2,22]]},"abstract":"<jats:p><jats:named-content content-type=\"genus-species\">E. coli<\/jats:named-content>ST95 is one of five dominant ExPEC lineages globally and noted for causing urinary tract and bloodstream infections and neonatal meningitis in humans and colibacillosis in poultry. Using high-resolution phylogenomics, we show that F replicon sequence type is linked to ST95 clade structure and zoonotic potential.<\/jats:p>","DOI":"10.1128\/msystems.01212-21","type":"journal-article","created":{"date-parts":[[2022,1,25]],"date-time":"2022-01-25T14:36:06Z","timestamp":1643121366000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":31,"title":["F Plasmid Lineages in Escherichia coli ST95: Implications for Host Range, Antibiotic Resistance, and Zoonoses"],"prefix":"10.1128","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9333-7160","authenticated-orcid":true,"given":"Max Laurence","family":"Cummins","sequence":"first","affiliation":[{"name":"The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia"},{"name":"Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6872-330X","authenticated-orcid":true,"given":"Cameron J.","family":"Reid","sequence":"additional","affiliation":[{"name":"The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia"},{"name":"Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9301-5372","authenticated-orcid":true,"given":"Steven Philip","family":"Djordjevic","sequence":"additional","affiliation":[{"name":"The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia"},{"name":"Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00347-10"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-021-05981-4"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1097\/INF.0000000000002976"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms9030526"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2504.180944"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1067\/mda.2003.7"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00135-18"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/microbiolspec.UTI-0006-2012"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.03050"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.fm.2018.01.003"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00470-18"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms9030567"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00248-020-01542-5"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00390-16"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-20988-w"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2013.00029"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000295"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cis502"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciu785"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004776"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(19)30273-7"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02693-18"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijerph17093061"},{"key":"e_1_3_2_25_2","volume-title":"Escherichia coli: pathotypes and principles of pathogenesis.","author":"Donnenberg M","year":"2013","unstructured":"Donnenberg M. 2013. Escherichia coli: pathotypes and principles of pathogenesis. Academic Press, London, United Kingdom."},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2011.03497.x"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cis929"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1096\/fj.09-144972"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2412.180272"},{"key":"e_1_3_2_30_2","first-page":"18","article-title":"Clinical and microbiological profile of infections during induction phase of acute myeloid leukemia","volume":"1","author":"Parikh S","year":"2018","unstructured":"Parikh S, Goswami P, Anand A, Panchal H, Patel A, Kulkarni R, Shastri B. 2018. Clinical and microbiological profile of infections during induction phase of acute myeloid leukemia. Gulf J Oncolog 1:18\u201323.","journal-title":"Gulf J Oncolog"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000371"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1086\/375347"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.01333-08"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics9110782"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01610-20"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1089\/mdr.2017.0177"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00333-18"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000250"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00816-08"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.188.2.745-758.2006"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2011.0961"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00363-06"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.023143-0"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkz484"},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2018.06.017"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2009.0266"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.25911\/5d67b4b42d2b5"},{"key":"e_1_3_2_48_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.01260-09"},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.01241-15"},{"key":"e_1_3_2_50_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00168-17"},{"key":"e_1_3_2_51_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-020-0416-x"},{"key":"e_1_3_2_52_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01025-12"},{"key":"e_1_3_2_53_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-014-0203-9"},{"key":"e_1_3_2_54_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.69.7.4572-4579.2001"},{"key":"e_1_3_2_55_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.plasmid.2009.10.003"},{"key":"e_1_3_2_56_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0180599"},{"key":"e_1_3_2_57_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1711842115"},{"key":"e_1_3_2_58_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijerph7010089"},{"key":"e_1_3_2_59_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetmic.2013.08.007"},{"key":"e_1_3_2_60_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0169589"},{"key":"e_1_3_2_61_2","doi-asserted-by":"publisher","DOI":"10.1016\/s0168-1605(02)00028-4"},{"key":"e_1_3_2_62_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.plasmid.2016.02.002"},{"key":"e_1_3_2_63_2","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms5030050"},{"key":"e_1_3_2_64_2","volume-title":"Food outlook: biannual report on global food markets, October 2014.","author":"Food and Agriculture Organization of the United Nations. Trade and Markets Division.","year":"2014","unstructured":"Food and Agriculture Organization of the United Nations. Trade and Markets Division. 2014. Food outlook: biannual report on global food markets, October 2014. Food and Agriculture Organization of the United Nations, Rome, Italy."},{"key":"e_1_3_2_65_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijerph16193521"},{"key":"e_1_3_2_66_2","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2007.0026"},{"key":"e_1_3_2_67_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00981-09"},{"key":"e_1_3_2_68_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2672.1986.tb04278.x"},{"key":"e_1_3_2_69_2","volume-title":"Benefits and risks of the use of chlorine-containing disinfectants in food production and food processing: report of a joint FAO\/WHO expert meeting, Ann Arbor, MI, USA, 27\u201330 May 2008.","author":"World Health Organization.","year":"2009","unstructured":"World Health Organization. 2009. Benefits and risks of the use of chlorine-containing disinfectants in food production and food processing: report of a joint FAO\/WHO expert meeting, Ann Arbor, MI, USA, 27\u201330 May 2008. World Health Organization, Geneva, Switzerland."},{"key":"e_1_3_2_70_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0015524"},{"key":"e_1_3_2_71_2","doi-asserted-by":"publisher","DOI":"10.1007\/82_2012_303"},{"key":"e_1_3_2_72_2","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-92-2-335"},{"key":"e_1_3_2_73_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.00387"},{"key":"e_1_3_2_74_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0078862"},{"key":"e_1_3_2_75_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgar.2015.08.002"},{"key":"e_1_3_2_76_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01118-20"},{"key":"e_1_3_2_77_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.02267"},{"key":"e_1_3_2_78_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0172997"},{"key":"e_1_3_2_79_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00038-16"},{"key":"e_1_3_2_80_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00743-20"},{"key":"e_1_3_2_81_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02601-16"},{"key":"e_1_3_2_82_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgar.2020.03.018"},{"key":"e_1_3_2_83_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00121-16"},{"key":"e_1_3_2_84_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0600938103"},{"key":"e_1_3_2_85_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2015.11.010"},{"key":"e_1_3_2_86_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.251678.119"},{"key":"e_1_3_2_87_2","doi-asserted-by":"crossref","unstructured":"Zhou Z Alikhan N-F Mohamed K Fan Y Achtman M the Agama Study Group. 2019. The user\u2019s guide to comparative genomics with EnteroBase including case studies on transmissions of micro-clades of Salmonella the phylogeny of ancient and modern Yersinia pestis genomes and the core genomic diversity of all Escherichia. bioRxiv 613554. doi:10.1101\/613554.","DOI":"10.1101\/613554"},{"key":"e_1_3_2_88_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx713"},{"key":"e_1_3_2_89_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv421"},{"key":"e_1_3_2_90_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000056"},{"key":"e_1_3_2_91_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw256"},{"key":"e_1_3_2_92_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4285"},{"key":"e_1_3_2_93_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msx281"},{"key":"e_1_3_2_94_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz361"},{"key":"e_1_3_2_95_2","volume-title":"R: a language and environment for statistical computing.","author":"R Core Team","year":"2013","unstructured":"R Core Team. 2013. R: a language and environment for statistical computing. The R Foundation, Vienna, Austria."},{"key":"e_1_3_2_96_2","doi-asserted-by":"publisher","DOI":"10.1111\/2041-210X.12628"},{"key":"e_1_3_2_97_2","doi-asserted-by":"crossref","unstructured":"Wickham H Francois R Henry L M\u00fcller K. 2015. Dplyr: a grammar of data manipulation. R package version 04 3.","DOI":"10.32614\/CRAN.package.dplyr"},{"key":"e_1_3_2_98_2","doi-asserted-by":"crossref","unstructured":"Bache SM Wickham H. 2014. Magrittr: a forward-pipe operator for R. R package version 1.","DOI":"10.32614\/CRAN.package.magrittr"},{"key":"e_1_3_2_99_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-24277-4"},{"key":"e_1_3_2_100_2","unstructured":"Wickham H Hester J Francois R. 2017. Readr: read rectangular text data. R package version 1:1."},{"key":"e_1_3_2_101_2","unstructured":"Wickham H. 2012. Reshape2: Flexibly reshape data: a reboot of the reshape package. R package version 1."},{"key":"e_1_3_2_102_2","unstructured":"Yu G. 2019. A tidy tool for phylogenetic tree data manipulation [R package tidytree version 0.1. 9]. Comprehensive R Archive Network."},{"key":"e_1_3_2_103_2","doi-asserted-by":"crossref","unstructured":"Yu G. 2017. Ggimage: use Image in \u2018Ggplot2.\u2019","DOI":"10.32614\/CRAN.package.ggimage"},{"key":"e_1_3_2_104_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkx217"},{"key":"e_1_3_2_105_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz935"},{"key":"e_1_3_2_106_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki008"},{"key":"e_1_3_2_107_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkj014"},{"key":"e_1_3_2_108_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02412-14"},{"key":"e_1_3_2_109_2","volume-title":"Critically important antimicrobials for human medicine.","author":"World Health Organization.","year":"2019","unstructured":"World Health Organization. 2019. Critically important antimicrobials for human medicine. World Health Organization, Geneva, Switzerland."},{"key":"e_1_3_2_110_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-9877-7_20"}],"updated-by":[{"DOI":"10.1128\/msystems.00210-22","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2022,3,21]],"date-time":"2022-03-21T00:00:00Z","timestamp":1647820800000}}],"container-title":["mSystems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.01212-21","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.01212-21","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,16]],"date-time":"2024-09-16T20:58:38Z","timestamp":1726520318000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/msystems.01212-21"}},"subtitle":[],"editor":[{"given":"Suleyman","family":"Yildirim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,2,22]]},"references-count":109,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2022,2,22]]}},"alternative-id":["10.1128\/msystems.01212-21"],"URL":"https:\/\/doi.org\/10.1128\/msystems.01212-21","relation":{"correction":[{"id-type":"doi","id":"10.1128\/msystems.00210-22","asserted-by":"object"}]},"ISSN":["2379-5077"],"issn-type":[{"value":"2379-5077","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,2,22]]},"assertion":[{"value":"2021-10-05","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-12-22","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-01-25","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01212-21"}}