{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T16:03:09Z","timestamp":1790265789364,"version":"4.1.0"},"reference-count":44,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2020,4,3]],"date-time":"2020-04-03T00:00:00Z","timestamp":1585872000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003549","name":"Hungarian Scientific Research Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003549","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012550","name":"Nemzeti Kutat\u00e1si, Fejleszt\u00e9si\u00e9s Innovaci\u00f3s Alap","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012550","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"DOI":"10.3389\/fmicb.2020.00539","type":"journal-article","created":{"date-parts":[[2020,4,3]],"date-time":"2020-04-03T15:02:20Z","timestamp":1585926140000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":20,"title":["Comparative Genome Analysis of Hungarian and Global Strains of Salmonella Infantis"],"prefix":"10.3389","volume":"11","author":[{"given":"Tibor","family":"Nagy","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ama","family":"Szmolka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T\u00edmea","family":"Wilk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00e1nos","family":"Kiss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M\u00f3nika","family":"Szab\u00f3","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Judit","family":"P\u00e1szti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"B\u00e9la","family":"Nagy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ferenc","family":"Olasz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2020,4,3]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijfoodmicro.2019.108275","article-title":"Genome analysis of antimicrobial resistance, virulence, and plasmid presence in Turkish Salmonella serovar Infantis isolates.","volume":"307","author":"Acar","year":"2019","journal-title":"Int. J. Food. Microbiol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"D7","DOI":"10.1093\/nar\/gkv1290","article-title":"Database resources of the national center for biotechnology information.","volume":"44","author":"Agarwala","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"B3","doi-asserted-by":"publisher","first-page":"214","DOI":"10.4315\/0362-028x-69.1.214","article-title":"Antimicrobial resistance types and genes in Salmonella enterica infantis isolates from retail raw chicken meat and broiler chickens on farms.","volume":"69","author":"Asai","year":"2006","journal-title":"J. Food Prot."},{"key":"B4","doi-asserted-by":"publisher","first-page":"977","DOI":"10.1111\/1462-2920.12351","article-title":"A unique megaplasmid contributes to stress tolerance and pathogenicity of an emergent Salmonella enterica serovar Infantis strain.","volume":"16","author":"Aviv","year":"2014","journal-title":"Environ. Microbiol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"W30","DOI":"10.1093\/nar\/gkx343","article-title":"IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets.","volume":"45","author":"Bertelli","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijfoodmicro.2019.108497","article-title":"Mega-plasmid found worldwide confers multiple antimicrobial resistance in Salmonella Infantis of broiler origin in Russia.","volume":"26","author":"Bogomazova","year":"2019","journal-title":"Int. J. Food Microbiol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"1125","DOI":"10.1099\/00221287-139-6-1125","article-title":"Salmonella reference collection B (SARB): strains of 37 serovars of subspecies I","volume":"139","author":"Boyd","year":"1993","journal-title":"J. Gen. Microbiol"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications.","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"B10","doi-asserted-by":"publisher","first-page":"1872","DOI":"10.1128\/aac.01514-06","article-title":"Dissemination of an extended-spectrum-beta-lactamase bla(TEM-52) gene-carrying IncI1 plasmid in various Salmonella enterica serovars isolated from poultry and humans in Belgium and France between 2001 and 2005.","volume":"51","author":"Cloeckaert","year":"2007","journal-title":"Antimicrob. Agents Chemother."},{"key":"B11","doi-asserted-by":"publisher","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":"B12","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1016\/j.ijantimicag.2011.07.001","article-title":"Molecular characterisation of multidrug-resistant Salmonella enterica serotype Infantis from humans, animals and the environment in Italy.","volume":"38","author":"Dionisi","year":"2011","journal-title":"Int. J. Antimicrob. Agents"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.2903\/j.efsa.2017.4694","article-title":"The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2015.","volume":"15","year":"","journal-title":"EFSA J."},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.2903\/j.efsa.2017.5077","article-title":"The European Union summary report on trends and sources of zoonoses, zoonotic agents and food\u2212borne outbreaks in 2016.","volume":"15","year":"","journal-title":"."},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.2903\/j.efsa.2019.5598","article-title":"The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2017.","volume":"17","year":"2019","journal-title":"EFSA J."},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002191","article-title":"Salmonella bongori provides insights into the evolution of the Salmonellae.","volume":"7","author":"Fookes","year":"2011","journal-title":"PLoS Pathog."},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0144802","article-title":"Emergence of a clonal lineage of multidrug-resistant ESBL-Producing Salmonella Infantis Transmitted from broilers and broiler meat to humans in Italy between 2011 and 2014.","volume":"10","author":"Franco","year":"2015","journal-title":"PLoS One"},{"key":"B18","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.3201\/eid1611.100100","article-title":"Multidrug-resistant Salmonella enterica serovar Infantis.","volume":"16","author":"Gal-Mor","year":"2010","journal-title":"Israel. Emerg. Infect. Dis."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.01322","article-title":"Salmonella enterica serovar infantis from food and human infections, Switzerland, 2010-2015: poultry-related multidrug resistant clones and an emerging ESBL producing clonal lineage.","volume":"8","author":"Hindermann","year":"2017","journal-title":"Front. Microbiol."},{"key":"B20","doi-asserted-by":"publisher","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":"B21","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-4601-5","article-title":"Clustering of Pan- and core-genome of lactobacillus provides novel evolutionary insights for differentiation.","volume":"19","author":"Inglin","year":"2018","journal-title":"BMC Genomics"},{"key":"B22","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1111\/j.1472-765X.2007.02220.x","article-title":"Novel PCR assay for identification of Salmonella enterica serovar Infantis.","volume":"45","author":"Kardos","year":"2007","journal-title":"Lett. Appl. Microbiol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1128\/jcm.06094-11","article-title":"Multilocus sequence typing of total-genome-sequenced bacteria.","volume":"50","author":"Larsen","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"D19","DOI":"10.1093\/nar\/gkq1019","article-title":"The sequence read archive.","volume":"39","author":"Leinonen","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.02604","article-title":"Comprehensive analysis reveals two distinct evolution patterns of Salmonella flagellin gene clusters.","volume":"8","author":"Liu","year":"2017","journal-title":"Front. Microbiol."},{"key":"B26","first-page":"155","article-title":"Features of Salmonella serovars among food handlers in Kyushu.","volume":"30","author":"Murakami","year":"2007","journal-title":"Japan. New Microbiol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1016\/j.ijfoodmicro.2008.07.005","article-title":"Prevalence and characterization of Salmonella infantis isolates originating from different points of the broiler chicken-human food chain in Hungary.","volume":"127","author":"N\u00f3gr\u00e1dy","year":"2008","journal-title":"Int. J. Food Microbiol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1016\/j.ijfoodmicro.2012.04.007","article-title":"Multidrug resistant clones of Salmonella Infantis of broiler origin in Europe.","volume":"157","author":"N\u00f3gr\u00e1dy","year":"2012","journal-title":"Int. J. Food Microbiol."},{"key":"B29","doi-asserted-by":"publisher","first-page":"645","DOI":"10.1093\/jac\/dkm249","article-title":"Emergence of multidrug-resistant clones of Salmonella Infantis in broiler chickens and humans in hungary.","volume":"60","author":"N\u00f3gr\u00e1dy","year":"2007","journal-title":"J. Antimicrob. Chemother."},{"key":"B30","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1093\/cid\/cis967","article-title":"The \u201cdecline and fall\u201d of nontyphoidal Salmonella in the United Kingdom.","volume":"56","author":"O\u2019Brien","year":"2013","journal-title":"Clin. Infect. Dis."},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.01468-14","article-title":"Genome Sequences of Three Salmonella enterica subsp. enterica serovar infantis strains from healthy broiler chicks in hungary and in the United Kingdom.","volume":"3","author":"Olasz","year":"2015","journal-title":"Genome Announc"},{"key":"B32","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis.","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-5137-4","article-title":"Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources.","volume":"19","author":"Pornsukarom","year":"2018","journal-title":"BMC Genomics"},{"key":"B34","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation.","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B35","doi-asserted-by":"publisher","first-page":"515","DOI":"10.1089\/fpd.2009.0454","article-title":"Detection and characterization of extended-spectrum beta-lactamase (TEM-52)-producing Salmonella serotype Infantis from broilers in Japan.","volume":"7","author":"Shahada","year":"2010","journal-title":"Foodborne Pathog. Dis."},{"key":"B36","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1016\/j.ijantimicag.2006.07.003","article-title":"Molecular epidemiology of antimicrobial resistance among Salmonella enterica serovar Infantis from poultry in Kagoshima, Japan.","volume":"28","author":"Shahada","year":"2006","journal-title":"Int. J. Antimicrob. Agents"},{"key":"B37","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/j.fm.2017.03.011","article-title":"Molecular epidemiology of the endemic multiresistance plasmid pSI54\/04 of Salmonella Infantis in broiler and human population in Hungary.","volume":"71","author":"Szmolka","year":"2018","journal-title":"Food Microbiol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"e488","DOI":"10.1128\/AAC.00488-17","article-title":"Comparative analysis of extended-spectrum-\u03b2-Lactamase CTX-M-65-producing salmonella enterica serovar infantis isolates from humans, food animals, and retail chickens in the United States.","volume":"61","author":"Tate","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.01400-16","article-title":"Genome Sequences of Multidrug-Resistant Salmonella enterica subsp. enterica Serovar Infantis Strains from Broiler Chicks in Hungary.","volume":"4","author":"Wilk","year":"2016","journal-title":"Genome Announc"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.01735-16","article-title":"Genome Sequences of Salmonella enterica subsp. enterica serovar infantis strains from hungary representing two peak incidence periods in three decades.","volume":"5","author":"Wilk","year":"2017","journal-title":"Genome Announc"},{"key":"B41","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1016\/j.meegid.2014.06.012","article-title":"Phylogenetic and population genetic analysis of Salmonella enterica subsp enterica serovar Infantis strains isolated in Japan using whole genome sequence data.","volume":"27","author":"Yokoyama","year":"2014","journal-title":"Infect. Genet. Evol."},{"key":"B42","doi-asserted-by":"publisher","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes.","volume":"67","author":"Zankari","year":"2012","journal-title":"J Antimicrob Chemother."},{"key":"B43","doi-asserted-by":"publisher","first-page":"1685","DOI":"10.1128\/jcm.00323-15","article-title":"Salmonella serotype determination utilizing high-throughput genome sequencing data.","volume":"53","author":"Zhang","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0055988","article-title":"Identification of genes to differentiate closely related Salmonella lineages.","volume":"8","author":"Zou","year":"2013","journal-title":"PLoS One"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmicb.2020.00539\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,4,3]],"date-time":"2020-04-03T15:02:24Z","timestamp":1585926144000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmicb.2020.00539\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,4,3]]},"references-count":44,"alternative-id":["10.3389\/fmicb.2020.00539"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2020.00539","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,4,3]]},"article-number":"539"}}