{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T04:15:46Z","timestamp":1793160946822,"version":"4.5.0"},"reference-count":67,"publisher":"Microbiology Society","issue":"7","license":[{"start":{"date-parts":[[2021,7,28]],"date-time":"2021-07-28T00:00:00Z","timestamp":1627430400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"project grant from the National Health and Medical Research Council of Australia","award":["1129713"],"award-info":[{"award-number":["1129713"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,28]]},"abstract":"\n \n \n Salmonella enterica<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n serovar Enteritidis is a major cause of foodborne\n \n \n Salmonella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n infections and outbreaks in humans. Effective surveillance and timely outbreak detection are essential for public health control. Multilevel genome typing (MGT) with multiple levels of resolution has been previously demonstrated as a promising tool for this purpose. In this study, we developed MGT with nine levels for\n S<\/jats:italic>\n . Enteritidis and characterised the genomic epidemiology of\n S<\/jats:italic>\n . Enteritidis in detail. We examined 26\u200a670 publicly available\n S<\/jats:italic>\n . Enteritidis genome sequences from isolates spanning 101\u2009years from 86 countries to reveal their spatial and temporal distributions. Using the lower resolution MGT levels, globally prevalent and regionally restricted sequence types (STs) were identified; avian associated MGT4-STs were found that were common in human cases in the USA; temporal trends were observed in the UK with MGT5-STs from 2014 to 2018 revealing both long lived endemic STs and the rapid expansion of new STs. Using MGT3 to MGT6, we identified multidrug resistance (MDR) associated STs at various MGT levels, which improves precision of detection and global tracking of MDR clones. We also found that the majority of the global\n S<\/jats:italic>\n . Enteritidis population fell within two predominant lineages, which had significantly different propensity of causing large scale outbreaks. An online open MGT database has been established for unified international surveillance of\n S<\/jats:italic>\n . Enteritidis. We demonstrated that MGT provides a flexible and high-resolution genome typing tool for\n S<\/jats:italic>\n . Enteritidis surveillance and outbreak detection.\n <\/jats:p>","DOI":"10.1099\/mgen.0.000605","type":"journal-article","created":{"date-parts":[[2021,7,22]],"date-time":"2021-07-22T09:16:14Z","timestamp":1626945374000},"source":"Crossref","is-referenced-by-count":17,"title":["Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing"],"prefix":"10.1099","volume":"7","author":[{"given":"Lijuan","family":"Luo","sequence":"first","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1911-7033","authenticated-orcid":false,"given":"Michael","family":"Payne","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandeep","family":"Kaur","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dalong","family":"Hu","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3559-6097","authenticated-orcid":false,"given":"Liam","family":"Cheney","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8506-9127","authenticated-orcid":false,"given":"Sophie","family":"Octavia","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinning","family":"Wang","sequence":"additional","affiliation":[{"name":"Centre for Infectious Diseases and Microbiology\u2013Public Health, Institute of Clinical Pathology and Medical Research \u2013 NSW Health Pathology, Westmead Hospital, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark M.","family":"Tanaka","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vitali","family":"Sintchenko","sequence":"additional","affiliation":[{"name":"Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, University of Sydney, New South Wales, Australia"},{"name":"Centre for Infectious Diseases and Microbiology\u2013Public Health, Institute of Clinical Pathology and Medical Research \u2013 NSW Health Pathology, Westmead Hospital, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9834-5258","authenticated-orcid":false,"given":"Ruiting","family":"Lan","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.15585\/mmwr.ss6710a1"},{"key":"R2","volume-title":"ECDC. Annual epidemiological report for 2017","year":"2020"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(19)30047-7"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.4315\/0362-028X.JFP-18-494"},{"key":"R5","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1038\/ng.3644","article-title":"Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings","volume":"48","author":"Feasey","year":"2016","journal-title":"Nat Genet, Article"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-019-3963-x"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.3382\/ps\/pew144"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0006156"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1017\/S0950268817001212"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.3201\/eid2009.131095"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0191042"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002776"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1007261"},{"key":"R14","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1101\/gr.251678.119","article-title":"The EnteroBase user\u2019s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity","volume":"30","author":"Zhou","year":"2020","journal-title":"Genome Res"},{"key":"R15","article-title":"Revolutionising public health reference microbiology using whole genome sequencing: Salmonella as an exemplar","author":"Ashton","year":"2015","journal-title":"bioRxiv"},{"key":"R16","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btab234","article-title":"HierCC: A multi-level clustering scheme for population assignments based on core genome MLST","author":"Zhou","year":"2021","journal-title":"Bioinformatics"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.3201\/eid2501.180835"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02332-14"},{"key":"R19","doi-asserted-by":"crossref","first-page":"17","DOI":"10.2807\/1560-7917.ES.2017.22.50.17-00196","article-title":"Re-evaluation of a 2014 multi-country European outbreak of Salmonella Enteritidis phage type 14b using recent epidemiological and molecular data","volume":"22","author":"Hormansdorfer","year":"2017","journal-title":"Euro Surveill"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2020.25.20.1900519"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt086"},{"key":"R22","article-title":"Comprehensive assessment of the quality of Salmonella whole genome sequence data available in public sequence databases using the Salmonella In silico Typing Resource (SISTR)","volume":"4","author":"Robertson","year":"2018","journal-title":"Microb Genom"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1540-z"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2014-15-3-r46"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00323-15"},{"key":"R28","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0147101"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"R30","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1073\/pnas.1201061109","article-title":"The transcriptional landscape and small rnas of Salmonella enterica serovar Typhimurium","volume":"109","author":"Kroger","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.3163\/1536-5050.104.2.022"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dks261"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02412-14"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0524-x"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009490"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1196"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msz241"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/vey016"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syy032"},{"key":"R40","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1093\/nar\/gki008","article-title":"VFDB: A reference database for bacterial virulence factors","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"R41","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijfoodmicro.2020.108831"},{"key":"R42","doi-asserted-by":"publisher","DOI":"10.2307\/2332226"},{"key":"R43","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro904"},{"key":"R44","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-18667-2","article-title":"Salmonella Enteritidis ST183: emerging and endemic biotypes affecting western European hedgehogs (Erinaceus europaeus) and people in Great Britain","volume":"8","author":"Lawson","year":"2018","journal-title":"Sci Rep"},{"key":"R45","doi-asserted-by":"publisher","DOI":"10.1016\/j.fm.2017.04.005"},{"key":"R46","doi-asserted-by":"crossref","DOI":"10.1099\/mgen.0.000310","article-title":"Enhancing genomics-based outbreak detection of endemic Salmonella enterica serovar Typhimurium using dynamic thresholds","author":"Payne","year":"2019","journal-title":"Microb Genom"},{"issue":"317","key":"R47","article-title":"The transformation of reference microbiology methods and surveillance for Salmonella with the use of whole genome sequencing in England and Wales","volume":"7","author":"Chattaway","year":"2019","journal-title":"Front Pub Health"},{"key":"R48","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.es2015.20.16.21098"},{"key":"R49","doi-asserted-by":"publisher","DOI":"10.1017\/S0950268816001941"},{"key":"R50","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2011.00129"},{"key":"R51","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-019-1543-2"},{"key":"R52","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000070"},{"key":"R53","doi-asserted-by":"publisher","DOI":"10.13031\/jash.12756"},{"key":"R54","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.03407-14"},{"key":"R55","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01280-15"},{"key":"R56","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.00729"},{"key":"R57","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2019.00298"},{"key":"R58","doi-asserted-by":"publisher","DOI":"10.1089\/mdr.2018.0421"},{"key":"R59","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0007485"},{"key":"R60","doi-asserted-by":"publisher","DOI":"10.1128\/aem.66.11.4854-4862.2000"},{"key":"R61","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.02431"},{"key":"R62","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.00715"},{"key":"R63","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02746-15"},{"key":"R64","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkn131"},{"key":"R65","doi-asserted-by":"publisher","DOI":"10.1292\/jvms.11-0488"},{"key":"R66","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-020-00836-1"},{"key":"R67","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.05497-11"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000605?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,14]],"date-time":"2023-12-14T17:29:54Z","timestamp":1702574994000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000605"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,7,28]]},"references-count":67,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2021,7,28]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.000605","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.06.30.169953","asserted-by":"object"}]},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,7,28]]}}}