10.3389/fmicb.2018.00836.s004 Walid Mottawea Walid Mottawea Marc-Olivier Duceppe Marc-Olivier Duceppe Andrée A. Dupras Andrée A. Dupras Valentine Usongo Valentine Usongo Julie Jeukens Julie Jeukens Luca Freschi Luca Freschi Jean-Guillaume Emond-Rheault Jean-Guillaume Emond-Rheault Jeremie Hamel Jeremie Hamel Irena Kukavica-Ibrulj Irena Kukavica-Ibrulj Brian Boyle Brian Boyle Alexander Gill Alexander Gill Elton Burnett Elton Burnett Eelco Franz Eelco Franz Gitanjali Arya Gitanjali Arya Joel T. Weadge Joel T. Weadge Samantha Gruenheid Samantha Gruenheid Martin Wiedmann Martin Wiedmann Hongsheng Huang Hongsheng Huang France Daigle France Daigle Sylvain Moineau Sylvain Moineau Sadjia Bekal Sadjia Bekal Roger C. Levesque Roger C. Levesque Lawrence D. Goodridge Lawrence D. Goodridge Dele Ogunremi Dele Ogunremi Table_2_Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping.XLSX Frontiers 2018 Salmonella prophage sequence typing genome diversity outbreaks Enteritidis 2018-05-04 07:14:04 Dataset https://frontiersin.figshare.com/articles/dataset/Table_2_Salmonella_enterica_Prophage_Sequence_Profiles_Reflect_Genome_Diversity_and_Can_Be_Used_for_High_Discrimination_Subtyping_XLSX/6221897 <p>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.</p>