{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T22:30:37Z","timestamp":1775169037147,"version":"3.50.1"},"reference-count":23,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2018,2,5]],"date-time":"2018-02-05T00:00:00Z","timestamp":1517788800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0192233","type":"journal-article","created":{"date-parts":[[2018,2,5]],"date-time":"2018-02-05T13:33:08Z","timestamp":1517837588000},"page":"e0192233","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":9,"title":["Impact of the choice of reference genome on the ability of the core genome SNV methodology to distinguish strains of Salmonella enterica serovar Heidelberg"],"prefix":"10.1371","volume":"13","author":[{"given":"Valentine","family":"Usongo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chrystal","family":"Berry","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Khadidja","family":"Yousfi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florence","family":"Doualla-Bell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Genevieve","family":"Labb\u00e9","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roger","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Fournier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Celine","family":"Nadon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lawrence","family":"Goodridge","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9840-0114","authenticated-orcid":true,"given":"Sadjia","family":"Bekal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2018,2,5]]},"reference":[{"key":"ref1","unstructured":"The National Microbiology Laboratory (NML), Centre for Food-borne, Environmental and Zoonotic Infectious Diseases (CFEZID), Public Health Agency of Canada, Provincial Public Health Microbiology Laboratories. 2014. National Enteric Surveillance Program (NESP): annual summary 2012. Public Health Agency of Canada, Ottawa, Ontario, Canada."},{"key":"ref2","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1128\/JCM.02200-15","article-title":"Usefulness of High-Quality Core Genome Single-Nucleotide Variant Analysis for Subtyping the Highly Clonal and the Most Prevalent <italic>Salmonella enterica<\/italic> Serovar Heidelberg Clone in the Context of outbreak investigations","volume":"54","author":"S Bekal","year":"2016","journal-title":"J Clin Microbiol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1975","DOI":"10.1128\/JCM.00081-16","article-title":"Practical Value of Food Pathogen Traceability through Building a Whole Genome Sequencing Network and Database","volume":"54","author":"MW Allard","year":"2016","journal-title":"J Clin Microbiol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1038\/nrmicro3093","article-title":"MLST revisited: the gene-by-gene approach to bacterial genomics","volume":"11","author":"MC Maiden","year":"2013","journal-title":"Nat Rev Microbiol"},{"issue":"2","key":"ref5","doi-asserted-by":"crossref","first-page":"16185","DOI":"10.1038\/nmicrobiol.2016.185","article-title":"Whole genome-based population biology and epidemiological surveillance of <italic>Listeria monocytogenes<\/italic>","volume":"10\/10","author":"A Moura","year":"2016","journal-title":"Nat Microbiol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1128\/JCM.02344-15","article-title":"Prospective Whole-Genome Sequencing Enhances National Surveillance of <italic>Listeria monocytogenes<\/italic>","volume":"54","author":"JC Kwong","year":"2016","journal-title":"J Clin Microbiol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1093\/molbev\/msu088","article-title":"Automated reconstruction of whole-genome phylogenies from short-sequence reads","volume":"31","author":"F Bertels","year":"2014","journal-title":"Mol Biol Evol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its application to single cell sequencing","volume":"19","author":"A Bankevich","year":"2012","journal-title":"J Comput Biol"},{"key":"ref9","article-title":"Complete genome sequence of 17 Canadian isolates of <italic>Salmonella enterica subsp<\/italic>. enterica serovar Heidelberg from human, animal and food sources","volume":"15","author":"G Labb\u00e9","year":"2016","journal-title":"Genome Announce"},{"key":"ref10","doi-asserted-by":"crossref","unstructured":"Petkau A, Mabon P, Sieffert C, Knox NC, Cabral J, Iskander M, et al. SNVPhyl: A Single Nucleotide Variant Phylogenomics pipeline for microbial genomic epidemiology. BioRixV. 2016;bioRixv. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/doi.org\/10.1101\/092940\" xlink:type=\"simple\">https:\/\/doi.org\/10.1101\/092940<\/ext-link>.","DOI":"10.1101\/092940"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"W3","DOI":"10.1093\/nar\/gkw343","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update","volume":"44","author":"E Afgan","year":"2016","journal-title":"Nucl Acids Res"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"235","DOI":"10.3389\/fgene.2015.00235","article-title":"Best practices for evaluating single nucleotide variant calling methods for microbial genomics","volume":"6","author":"ND Olson","year":"2015","journal-title":"Front Genet"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: a better, faster version of the PHAST phage search tool","volume":"44","author":"D Arndt","year":"2016","journal-title":"Nucl Acids Res"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/1471-2105-13-87","article-title":"PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods","volume":"13","author":"AP Francisco","year":"2012","journal-title":"BMC Bioinform"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/0025-5564(81)90043-2","article-title":"Comparison of phylogenetic trees","volume":"53","author":"DF Robinson","year":"1981","journal-title":"Mathematical Biosciences"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"W573","DOI":"10.1093\/nar\/gks485","article-title":"T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks","volume":"40","author":"A Boc","year":"2012","journal-title":"Nucl Acids Res"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"e87791","DOI":"10.1371\/journal.pone.0087991","article-title":"Evaluation of whole genome sequencing for outbreak detection of <italic>Salmonella enterica<\/italic>","volume":"9","author":"P Leekitcharoenphon","year":"2014","journal-title":"PLoS One"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"235","DOI":"10.3389\/fgene.2015.00235","article-title":"Best practices for evaluating single nucleotide variant calling methods for microbial genomics","volume":"6","author":"ND Olson","year":"2015","journal-title":"Front Genet"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1007\/s10142-015-0433-4","article-title":"Insights from 20 years of bacterial genome sequencing","volume":"15","author":"M Land","year":"2015","journal-title":"Funct Integr Genomics"},{"key":"ref21","doi-asserted-by":"crossref","DOI":"10.1186\/1944-3277-9-20","article-title":"Quality scores for 32,000 genomes","volume":"9","author":"M Land","year":"2014","journal-title":"Stand Genomic Sci"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"30544","DOI":"10.2807\/1560-7917.ES.2017.22.23.30544","article-title":"PulseNet International: Vision for the implementation of whole genome sequencing (wgs) for global food-borne disease surveillance","volume":"22","author":"C Nadon","year":"2017","journal-title":"Euro Surveill"},{"key":"ref23","article-title":"Multi-provincial Salmonellosis outbreak related to newly hatched chicks and poults. A genomics perspective","volume":"1","author":"MA Croxen","year":"2017","journal-title":"PLoSCurr"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0192233","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,24]],"date-time":"2018-10-24T00:41:26Z","timestamp":1540341686000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0192233"}},"subtitle":[],"editor":[{"given":"Jo\u00ebl","family":"Mossong","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,2,5]]},"references-count":23,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2018,2,5]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0192233","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,2,5]]}}}