{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T23:36:55Z","timestamp":1779233815224,"version":"3.51.4"},"reference-count":34,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2022,11,11]],"date-time":"2022-11-11T00:00:00Z","timestamp":1668124800000},"content-version":"vor","delay-in-days":314,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["1129713"],"award-info":[{"award-number":["1129713"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["211806"],"award-info":[{"award-number":["211806"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Multilevel genome typing (MGT) enables the genomic characterization of bacterial isolates and the relationships among them. The MGT system describes an isolate using multiple multilocus sequence typing (MLST) schemes, referred to as levels. Thus, for a new isolate, sequence types (STs) assigned at multiple precisely defined levels can be used to type isolates at multiple resolutions. The MGT designation for isolates is stable, and the assignment is faster than the existing approaches. MGT\u2019s utility has been demonstrated in multiple species. This paper presents a publicly accessible web service called MGTdb, which enables the assignment of MGT STs to isolates, along with their storage, retrieval and analysis. The MGTdb web service enables upload of genome data as sequence reads or alleles, which are processed and assigned MGT identifiers. Additionally, any newly sequenced isolates deposited in the National Center for Biotechnology Information\u2019s Sequence Read Archive are also regularly retrieved (currently daily), processed, assigned MGT identifiers and made publicly available in MGTdb. Interactive visualization tools are presented to assist analysis, along with capabilities to download publicly available isolates and assignments for use with external software. MGTdb is currently available for Salmonella enterica serovars Typhimurium and Enteritidis and Vibrio cholerae. We demonstrate the usability of MGTdb through three case studies \u2014 to study the long-term national surveillance of S. Typhimurium, the local epidemiology and outbreaks of S. Typhimurium, and the global epidemiology of V. cholerae. Thus, MGTdb enables epidemiological and microbiological investigations at multiple levels of resolution for all publicly available isolates of these pathogens.<\/jats:p>\n                  <jats:p>Database URL: https:\/\/mgtdb.unsw.edu.au<\/jats:p>","DOI":"10.1093\/database\/baac094","type":"journal-article","created":{"date-parts":[[2022,10,18]],"date-time":"2022-10-18T08:46:01Z","timestamp":1666082761000},"source":"Crossref","is-referenced-by-count":14,"title":["MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens"],"prefix":"10.1093","volume":"2022","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0356-3151","authenticated-orcid":false,"given":"Sandeep","family":"Kaur","sequence":"first","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales , New South Wales 2052, Australia"},{"name":"School of Computer Science and Engineering, University of New South Wales , New South Wales 2052, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"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 , New South Wales 2052, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lijuan","family":"Luo","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales , New South Wales 2052, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sophie","family":"Octavia","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales , New South Wales 2052, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark M","family":"Tanaka","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales , New South Wales 2052, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vitali","family":"Sintchenko","sequence":"additional","affiliation":[{"name":"Centre for Infectious Diseases and Microbiology\u2014Public Health, Institute of Clinical Pathology and Medical Research\u2014NSW Health Pathology, Westmead Hospital , New South Wales 2145, Australia"},{"name":"Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, University of Sydney , New South Wales 2006, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"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 , New South Wales 2052, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,11,11]]},"reference":[{"key":"2022111111490669900_R1","article-title":"WHO recommended surveillance standards. 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