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>