{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T10:54:09Z","timestamp":1790506449537,"version":"4.1.0"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2019,7,22]],"date-time":"2019-07-22T00:00:00Z","timestamp":1563753600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"South Dakota Beef Industry Council"},{"name":"USDA National Institute of Food and Agriculture Hatch","award":["SD00H532-14"],"award-info":[{"award-number":["SD00H532-14"]}]},{"name":"USDA National Institute of Food and Agriculture Hatch","award":["SD00R540-15"],"award-info":[{"award-number":["SD00R540-15"]}]},{"name":"United States Food and Drug Administration GenomeTrakr"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Salmonella enterica serotype Dublin (S. Dublin) is a bovine-adapted serotype that can cause serious systemic infections in humans. Despite the increasing prevalence of human infections and the negative impact on agricultural processes, little is known about the population structure of the serotype. To this end, we compiled a manually curated data set comprising of 880 S. Dublin genomes. Core genome phylogeny and ancestral state reconstruction revealed that region-specific clades dominate the global population structure of S. Dublin. Strains of S. Dublin in the UK are genomically distinct from US, Brazilian, and African strains. The geographical partitioning impacts the composition of the core genome as well as the ancillary genome. Antibiotic resistance genes are almost exclusively found in US genomes and are mediated by an IncA\/C2 plasmid. Phage content and the S. Dublin virulence plasmid were strongly conserved in the serotype. Comparison of S. Dublin to a closely related serotype, S. enterica serotype Enteritidis, revealed that S. Dublin contains 82 serotype specific genes that are not found in S. Enteritidis. Said genes encode metabolic functions involved in the uptake and catabolism of carbohydrates and virulence genes associated with type VI secretion systems and fimbria assembly respectively.<\/jats:p>","DOI":"10.1093\/gbe\/evz158","type":"journal-article","created":{"date-parts":[[2019,7,18]],"date-time":"2019-07-18T15:18:27Z","timestamp":1563463107000},"page":"2220-2231","source":"Crossref","is-referenced-by-count":44,"title":["Geography Shapes the Population Genomics of Salmonella enterica Dublin"],"prefix":"10.1093","volume":"11","author":[{"given":"Gavin J","family":"Fenske","sequence":"first","affiliation":[{"name":"Department of Veterinary and Biomedical Sciences, South Dakota State University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anil","family":"Thachil","sequence":"additional","affiliation":[{"name":"Department of Population Medicine and Diagnostic Sciences, Cornell University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick L","family":"McDonough","sequence":"additional","affiliation":[{"name":"Department of Population Medicine and Diagnostic Sciences, Cornell University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amy","family":"Glaser","sequence":"additional","affiliation":[{"name":"Department of Population Medicine and Diagnostic Sciences, Cornell University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joy","family":"Scaria","sequence":"additional","affiliation":[{"name":"Department of Veterinary and Biomedical Sciences, South Dakota State University"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,7,22]]},"reference":[{"issue":"5","key":"2019082109151872900_evz158-B1","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell 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