Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping
Non-typhoidal is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (...
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Published in | Frontiers in microbiology Vol. 9; p. 836 |
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Main Authors | , , , , , , , , , , , , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
Switzerland
Frontiers Media S.A
04.05.2018
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Subjects | |
Online Access | Get full text |
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Summary: | Non-typhoidal
is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of
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
strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in
. In this study, the prophage sequence diversity in different
serovars and genetically related strains was investigated. Using whole genome sequences of 1,760 isolates of
representing 151
serovars and 66 closely related bacteria, prophage sequences were identified from assembled contigs using PHASTER. We detected 154 different prophages in
genomes. Prophage sequences were highly variable among
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
. 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
subtypes during foodborne outbreaks. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Edited by: Ludmila Chistoserdova, University of Washington, United States Reviewed by: Francisco Rodriguez-Valera, Universidad Miguel Hernández de Elche, Spain; Eric Altermann, AgResearch, New Zealand This article was submitted to Evolutionary and Genomic Microbiology, a section of the journal Frontiers in Microbiology |
ISSN: | 1664-302X 1664-302X |
DOI: | 10.3389/fmicb.2018.00836 |