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    Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping.

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    Authors
    Mottawea, Walid
    Duceppe, Marc-Olivier
    Dupras, Andrée A
    Usongo, Valentine
    Jeukens, Julie
    Freschi, Luca
    Emond-Rheault, Jean-Guillaume
    Hamel, Jeremie
    Kukavica-Ibrulj, Irena
    Boyle, Brian
    Gill, Alexander
    Burnett, Elton
    Franz, Eelco
    Arya, Gitanjali
    Weadge, Joel T
    Gruenheid, Samantha
    Wiedmann, Martin
    Huang, Hongsheng
    Daigle, France
    Moineau, Sylvain
    Bekal, Sadjia
    Levesque, Roger C
    Goodridge, Lawrence D
    Ogunremi, Dele
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    Type
    Article
    Language
    en
    
    Metadata
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    Title
    Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping.
    Published in
    Front Microbiol 2018; 9:836
    Publiekssamenvatting
    Non-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.
    DOI
    10.3389/fmicb.2018.00836
    PMID
    29780368
    URI
    http://hdl.handle.net/10029/621971
    ae974a485f413a2113503eed53cd6c53
    10.3389/fmicb.2018.00836
    Scopus Count
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