{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,27]],"date-time":"2025-09-27T08:18:43Z","timestamp":1758961123062},"reference-count":56,"publisher":"Elsevier BV","issue":"8","license":[{"start":{"date-parts":[[2011,12,1]],"date-time":"2011-12-01T00:00:00Z","timestamp":1322697600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"funder":[{"DOI":"10.13039\/100011094","name":"Public Health Agency of Canada","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100011094","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000146","name":"Alberta Innovates Technology Futures","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000146","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Infection, Genetics and Evolution"],"published-print":{"date-parts":[[2011,12]]},"DOI":"10.1016\/j.meegid.2011.09.021","type":"journal-article","created":{"date-parts":[[2011,10,2]],"date-time":"2011-10-02T00:44:33Z","timestamp":1317516273000},"page":"2151-2161","source":"Crossref","is-referenced-by-count":9,"title":["Identification of Salmonella enterica species- and subgroup-specific genomic regions using Panseq 2.0"],"prefix":"10.1016","volume":"11","author":[{"given":"Chad","family":"Laing","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andre","family":"Villegas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eduardo N.","family":"Taboada","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew","family":"Kropinski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James E.","family":"Thomas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Victor P.J.","family":"Gannon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.meegid.2011.09.021_b0005","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.meegid.2011.09.021_b0010","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1093\/bioinformatics\/btq665","article-title":"Mugsy: fast multiple alignment of closely related whole genomes","volume":"27","author":"Angiuoli","year":"2010","journal-title":"Bioinformatics"},{"issue":"Suppl. 1","key":"10.1016\/j.meegid.2011.09.021_b0015","doi-asserted-by":"crossref","first-page":"S29","DOI":"10.1086\/518143","article-title":"The genome of Salmonella enterica serovar Typhi","volume":"45","author":"Baker","year":"2007","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.meegid.2011.09.021_b0025","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1128\/AEM.01661-10","article-title":"Colonization of tomato plants by Salmonella enterica is cultivar dependent, and type 1 trichomes are preferred colonization sites","volume":"77","author":"Barak","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"issue":"8","key":"10.1016\/j.meegid.2011.09.021_b0035","doi-asserted-by":"crossref","first-page":"e800","DOI":"10.1371\/journal.pone.0000800","article-title":"Contribution of exogenous genetic elements to the group A Streptococcus metagenome","volume":"2","author":"Beres","year":"2007","journal-title":"PLoS ONE"},{"key":"10.1016\/j.meegid.2011.09.021_b0030","doi-asserted-by":"crossref","first-page":"4371","DOI":"10.1073\/pnas.0911295107","article-title":"Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics","volume":"107","author":"Beres","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.meegid.2011.09.021_b0040","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1016\/j.ympev.2009.08.010","article-title":"A whole-genome phylogeny of the family Pasteurellaceae","volume":"54","author":"Bonaventura","year":"2010","journal-title":"Mol. Phylogenet. Evol."},{"key":"10.1016\/j.meegid.2011.09.021_b0045","first-page":"91","article-title":"Salmonellosis: an epidemiologic study","volume":"7","author":"Broide","year":"2005","journal-title":"Isr. Med. Assoc. J."},{"key":"10.1016\/j.meegid.2011.09.021_b0050","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1111\/j.1574-6968.2009.01697.x","article-title":"Identification and distribution of accessory genome DNA sequences from an invasive African isolate of Salmonella Heidelberg","volume":"298","author":"Bronowski","year":"2009","journal-title":"FEMS Microbiol. Lett."},{"key":"10.1016\/j.meegid.2011.09.021_b0055","doi-asserted-by":"crossref","first-page":"2672","DOI":"10.1093\/bioinformatics\/btn529","article-title":"Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database","volume":"24","author":"Carver","year":"2008","journal-title":"Bioinformatics"},{"key":"10.1016\/j.meegid.2011.09.021_b0060","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1093\/bioinformatics\/btq010","article-title":"BamView: viewing mapped read alignment data in the context of the reference sequence","volume":"26","author":"Carver","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.meegid.2011.09.021_b0065","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1056\/NEJMoa1012928","article-title":"The origin of the Haitian cholera outbreak strain","volume":"364","author":"Chin","year":"2011","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.meegid.2011.09.021_b0070","doi-asserted-by":"crossref","first-page":"1690","DOI":"10.1093\/nar\/gki297","article-title":"The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen","volume":"33","author":"Chiu","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.meegid.2011.09.021_b0075","doi-asserted-by":"crossref","first-page":"8155","DOI":"10.1128\/JB.00636-08","article-title":"Characterization of the genomes of a diverse collection of Salmonella enterica serovar Typhimurium definitive phage type 104","volume":"190","author":"Cooke","year":"2008","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.meegid.2011.09.021_b0080","doi-asserted-by":"crossref","first-page":"e11147","DOI":"10.1371\/journal.pone.0011147","article-title":"ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement","volume":"5","author":"Darling","year":"2010","journal-title":"PLoS ONE"},{"key":"10.1016\/j.meegid.2011.09.021_b0020","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1186\/1471-2164-11-688","article-title":"Comparative genomics of the bacterial genus Listeria: genome evolution is characterized by limited gene acquisition and limited gene loss","volume":"11","author":"den Bakker","year":"2010","journal-title":"BMC Genomics"},{"key":"10.1016\/j.meegid.2011.09.021_b0090","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.tim.2010.04.002","article-title":"Impact of recombination on bacterial evolution","volume":"18","author":"Didelot","year":"2010","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.meegid.2011.09.021_b0085","doi-asserted-by":"crossref","first-page":"e1002191","DOI":"10.1371\/journal.pgen.1002191","article-title":"Recombination and population structure in Salmonella enterica","volume":"7","author":"Didelot","year":"2011","journal-title":"PLoS Genet."},{"key":"10.1016\/j.meegid.2011.09.021_b0095","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.meegid.2011.09.021_b0100","doi-asserted-by":"crossref","first-page":"2045","DOI":"10.1098\/rstb.2006.1925","article-title":"Mismatch induced speciation in Salmonella: model and data","volume":"361","author":"Falush","year":"2006","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"10.1016\/j.meegid.2011.09.021_b0105","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1056\/NEJMoa1003176","article-title":"Whole-genome sequencing and social-network analysis of a tuberculosis outbreak","volume":"364","author":"Gardy","year":"2011","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.meegid.2011.09.021_b0110","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1111\/j.1096-0031.2008.00217.x","article-title":"TNT, a free program for phylogenetic analysis","volume":"24","author":"Goloboff","year":"2008","journal-title":"Cladistics"},{"key":"10.1016\/j.meegid.2011.09.021_b0115","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0","volume":"59","author":"Guindon","year":"2010","journal-title":"Syst. Biol."},{"key":"10.1016\/j.meegid.2011.09.021_b0120","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1016\/j.meegid.2010.10.021","article-title":"Diversity of accessory genome of human and livestock-associated ST398 methicillin resistant Staphylococcus aureus strains","volume":"11","author":"Hallin","year":"2011","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.meegid.2011.09.021_b0125","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/1471-2164-10-36","article-title":"Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi","volume":"10","author":"Holt","year":"2009","journal-title":"BMC Genomics"},{"key":"10.1016\/j.meegid.2011.09.021_b0130","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1093\/molbev\/msj030","article-title":"Application of phylogenetic networks in evolutionary studies","volume":"23","author":"Huson","year":"2006","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.meegid.2011.09.021_b0135","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1186\/1471-2105-8-460","article-title":"Dendroscope: an interactive viewer for large phylogenetic trees","volume":"8","author":"Huson","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.meegid.2011.09.021_b0140","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1111\/j.1574-6976.2008.00136.x","article-title":"Genomic islands: tools of bacterial horizontal gene transfer and evolution","volume":"33","author":"Juhas","year":"2009","journal-title":"FEMS Microbiol. Rev."},{"key":"10.1016\/j.meegid.2011.09.021_b0145","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1101\/gr.229202. Article published online before March 2002","article-title":"BLAT-the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"10.1016\/j.meegid.2011.09.021_b0150","doi-asserted-by":"crossref","first-page":"e1001014","DOI":"10.1371\/journal.pbio.1001014","article-title":"Using BLAST to teach \u201cE-value-tionary\u201d concepts","volume":"9","author":"Kerfeld","year":"2011","journal-title":"PLoS Biol."},{"key":"10.1016\/j.meegid.2011.09.021_b0155","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/S1567-1348(02)00089-8","article-title":"Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000years old","volume":"2","author":"Kidgell","year":"2002","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.meegid.2011.09.021_b0160","doi-asserted-by":"crossref","first-page":"6142","DOI":"10.1128\/AEM.00138-06","article-title":"Comparison of Salmonella enterica serovar Typhimurium LT2 and non-LT2 Salmonella genomic sequences, and genotyping of salmonellae by using PCR","volume":"72","author":"Kim","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.meegid.2011.09.021_b0165","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol."},{"key":"10.1016\/j.meegid.2011.09.021_b0170","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1186\/1471-2105-11-461","article-title":"Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions","volume":"11","author":"Laing","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.meegid.2011.09.021_b0175","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1016\/j.meegid.2009.04.011","article-title":"Population structure, origins and evolution of major Salmonella enterica clones","volume":"9","author":"Lan","year":"2009","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.meegid.2011.09.021_b0180","doi-asserted-by":"crossref","first-page":"8713","DOI":"10.1073\/pnas.0812949106","article-title":"A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis","volume":"106","author":"Leopold","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.meegid.2011.09.021_b0185","doi-asserted-by":"crossref","first-page":"1282","DOI":"10.1016\/j.meegid.2010.07.021","article-title":"Further evidence of constrained radiation in the evolution of pathogenic Escherichia coli O157:H7","volume":"10","author":"Leopold","year":"2010","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.meegid.2011.09.021_b0190","doi-asserted-by":"crossref","first-page":"1132","DOI":"10.1016\/j.meegid.2010.07.015","article-title":"Association between phylogeny, virulence potential and serovars of Salmonella enterica","volume":"10","author":"Litrup","year":"2010","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.meegid.2011.09.021_b0195","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1007\/s00248-010-9717-3","article-title":"Comparison of 61 sequenced Escherichia coli genomes","volume":"60","author":"Lukjancenko","year":"2010","journal-title":"Microb. Ecol."},{"key":"10.1016\/j.meegid.2011.09.021_b0200","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/35101614","article-title":"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2","volume":"413","author":"McClelland","year":"2001","journal-title":"Nature"},{"key":"10.1016\/j.meegid.2011.09.021_b0205","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1016\/j.gde.2005.09.006","article-title":"The microbial pan-genome","volume":"15","author":"Medini","year":"2005","journal-title":"Curr. Opin. Genet. Dev."},{"key":"10.1016\/j.meegid.2011.09.021_b0210","doi-asserted-by":"crossref","first-page":"1140","DOI":"10.1038\/ng.705","article-title":"Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity","volume":"42","author":"Morelli","year":"2010","journal-title":"Nat. Genet."},{"key":"10.1016\/j.meegid.2011.09.021_b0215","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1186\/1471-2164-11-667","article-title":"Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes","volume":"11","author":"Nash","year":"2010","journal-title":"BMC Genomics"},{"key":"10.1016\/j.meegid.2011.09.021_b0220","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1016\/j.mib.2003.09.008","article-title":"Horizontal gene transfer and phylogenetics","volume":"6","author":"Philippe","year":"2003","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/j.meegid.2011.09.021_b0225","doi-asserted-by":"crossref","first-page":"i187","DOI":"10.1093\/bioinformatics\/btn281","article-title":"Segment-based multiple sequence alignment","volume":"24","author":"Rausch","year":"2008","journal-title":"Bioinformatics"},{"key":"10.1016\/j.meegid.2011.09.021_b0230","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1093\/bioinformatics\/16.10.944","article-title":"Artemis: sequence visualization and annotation","volume":"16","author":"Rutherford","year":"2000","journal-title":"Bioinformatics"},{"key":"10.1016\/j.meegid.2011.09.021_b0235","doi-asserted-by":"crossref","first-page":"6465","DOI":"10.1128\/JB.00969-10","article-title":"Evolution and population structure of Salmonella enterica serovar Newport","volume":"192","author":"Sangal","year":"2010","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.meegid.2011.09.021_b0240","doi-asserted-by":"crossref","first-page":"2262","DOI":"10.1128\/IAI.58.7.2262-2275.1990","article-title":"Evolutionary genetic relationships of clones of Salmonella serovars that cause human typhoid and other enteric fevers","volume":"58","author":"Selander","year":"1990","journal-title":"Infect. Immun."},{"key":"10.1016\/j.meegid.2011.09.021_b0245","doi-asserted-by":"crossref","first-page":"W194","DOI":"10.1093\/nar\/gkq326","article-title":"MGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes","volume":"38","author":"Shao","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.meegid.2011.09.021_b0250","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1093\/bioinformatics\/bti054","article-title":"Circular genome visualization and exploration using CGView","volume":"21","author":"Stothard","year":"2005","journal-title":"Bioinformatics"},{"key":"10.1016\/j.meegid.2011.09.021_b0255","doi-asserted-by":"crossref","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial \u201cpan-genome\u201d","volume":"102","author":"Tettelin","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.meegid.2011.09.021_b0260","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1186\/gb-2011-12-2-217","article-title":"The properties and applications of single-molecule DNA sequencing","volume":"12","author":"Thompson","year":"2011","journal-title":"Genome Biol."},{"key":"10.1016\/j.meegid.2011.09.021_b0265","doi-asserted-by":"crossref","first-page":"1624","DOI":"10.1101\/gr.077404.108","article-title":"Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287\/91 provides insights into evolutionary and host adaptation pathways","volume":"18","author":"Thomson","year":"2008","journal-title":"Genome Res."},{"key":"10.1016\/j.meegid.2011.09.021_b0270","doi-asserted-by":"crossref","first-page":"5568","DOI":"10.1128\/JB.187.16.5568-5577.2005","article-title":"Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae","volume":"187","author":"Vasconcelos","year":"2005","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.meegid.2011.09.021_b0275","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.tim.2010.10.003","article-title":"A species concept for bacteria based on adaptive divergence","volume":"19","author":"Vos","year":"2011","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.meegid.2011.09.021_b0280","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1093\/bioinformatics\/btq644","article-title":"GPU-BLAST: using graphics processors to accelerate protein sequence alignment","volume":"27","author":"Vouzis","year":"2011","journal-title":"Bioinformatics"}],"container-title":["Infection, Genetics and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1567134811003509?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1567134811003509?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2020,6,25]],"date-time":"2020-06-25T10:19:51Z","timestamp":1593080391000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1567134811003509"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,12]]},"references-count":56,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["S1567134811003509"],"URL":"https:\/\/doi.org\/10.1016\/j.meegid.2011.09.021","relation":{},"ISSN":["1567-1348"],"issn-type":[{"value":"1567-1348","type":"print"}],"subject":[],"published":{"date-parts":[[2011,12]]}}}