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dc.contributor.authorMottawea, Walid
dc.contributor.authorDuceppe, Marc-Olivier
dc.contributor.authorDupras, Andrée A
dc.contributor.authorUsongo, Valentine
dc.contributor.authorJeukens, Julie
dc.contributor.authorFreschi, Luca
dc.contributor.authorEmond-Rheault, Jean-Guillaume
dc.contributor.authorHamel, Jeremie
dc.contributor.authorKukavica-Ibrulj, Irena
dc.contributor.authorBoyle, Brian
dc.contributor.authorGill, Alexander
dc.contributor.authorBurnett, Elton
dc.contributor.authorFranz, Eelco
dc.contributor.authorArya, Gitanjali
dc.contributor.authorWeadge, Joel T
dc.contributor.authorGruenheid, Samantha
dc.contributor.authorWiedmann, Martin
dc.contributor.authorHuang, Hongsheng
dc.contributor.authorDaigle, France
dc.contributor.authorMoineau, Sylvain
dc.contributor.authorBekal, Sadjia
dc.contributor.authorLevesque, Roger C
dc.contributor.authorGoodridge, Lawrence D
dc.contributor.authorOgunremi, Dele
dc.date.accessioned2018-05-28T12:47:24Z
dc.date.available2018-05-28T12:47:24Z
dc.date.issued2018
dc.identifier.citationSalmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping. 2018, 9:836 Front Microbiolen
dc.identifier.issn1664-302X
dc.identifier.pmid29780368
dc.identifier.doi10.3389/fmicb.2018.00836
dc.identifier.urihttp://hdl.handle.net/10029/621971
dc.description.abstractNon-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP) typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella. In this study, the prophage sequence diversity in different Salmonella serovars and genetically related strains was investigated. Using whole genome sequences of 1,760 isolates of S. enterica representing 151 Salmonella serovars and 66 closely related bacteria, prophage sequences were identified from assembled contigs using PHASTER. We detected 154 different prophages in S. enterica genomes. Prophage sequences were highly variable among S. enterica serovars with a median ± interquartile range (IQR) of 5 ± 3 prophage regions per genome. While some prophage sequences were highly conserved among the strains of specific serovars, few regions were lineage specific. Therefore, strains belonging to each serovar could be clustered separately based on their prophage content. Analysis of S. Enteritidis isolates from seven outbreaks generated distinct prophage profiles for each outbreak. Taken altogether, the diversity of the prophage sequences correlates with genome diversity. Prophage repertoires provide an additional marker for differentiating S. enterica subtypes during foodborne outbreaks.
dc.language.isoenen
dc.rightsArchived with thanks to Frontiers in microbiologyen
dc.titleSalmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping.en
dc.typeArticleen
dc.identifier.journalFront Microbiol 2018; 9:836en
html.description.abstractNon-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP) typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella. In this study, the prophage sequence diversity in different Salmonella serovars and genetically related strains was investigated. Using whole genome sequences of 1,760 isolates of S. enterica representing 151 Salmonella serovars and 66 closely related bacteria, prophage sequences were identified from assembled contigs using PHASTER. We detected 154 different prophages in S. enterica genomes. Prophage sequences were highly variable among S. enterica serovars with a median ± interquartile range (IQR) of 5 ± 3 prophage regions per genome. While some prophage sequences were highly conserved among the strains of specific serovars, few regions were lineage specific. Therefore, strains belonging to each serovar could be clustered separately based on their prophage content. Analysis of S. Enteritidis isolates from seven outbreaks generated distinct prophage profiles for each outbreak. Taken altogether, the diversity of the prophage sequences correlates with genome diversity. Prophage repertoires provide an additional marker for differentiating S. enterica subtypes during foodborne outbreaks.


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