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Open AccessArticle

Diversity and Host Specificity Revealed by Biological Characterization and Whole Genome Sequencing of Bacteriophages Infecting Salmonella enterica

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Food, Nutrition and Health, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC G1V 0A6, Canada
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Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC G1V 0A6, Canada
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Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada
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Food Science Department, University of Guelph, Guelph, ON N1G 2W1, Canada
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Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
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Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC G1V 0A6, Canada
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Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany, and the Institute for Oceans and Fisheries, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Author to whom correspondence should be addressed.
Viruses 2019, 11(9), 854; https://doi.org/10.3390/v11090854
Received: 2 August 2019 / Revised: 5 September 2019 / Accepted: 5 September 2019 / Published: 14 September 2019
(This article belongs to the Special Issue The Application of Viruses to Biotechnology)
Phages infecting members of the opportunistic human pathogen, Salmonella enterica, are widespread in natural environments and offer a potential source of agents that could be used for controlling populations of this bacterium; yet, relatively little is known about these phages. Here we describe the isolation and characterization of 45 phages of Salmonella enterica from disparate geographic locations within British Columbia, Canada. Host-range profiling revealed host-specific patterns of susceptibility and resistance, with several phages identified that have a broad-host range (i.e., able to lyse >40% of bacterial hosts tested). One phage in particular, SE13, is able to lyse 51 out of the 61 Salmonella strains tested. Comparative genomic analyses also revealed an abundance of sequence diversity in the sequenced phages. Alignment of the genomes grouped the phages into 12 clusters with three singletons. Phages within certain clusters exhibited extraordinarily high genome homology (>98% nucleotide identity), yet between clusters, genomes exhibited a span of diversity (<50% nucleotide identity). Alignment of the major capsid protein also supported the clustering pattern observed with alignment of the whole genomes. We further observed associations between genomic relatedness and the site of isolation, as well as genetic elements related to DNA metabolism and host virulence. Our data support the knowledge framework for phage diversity and phage–host interactions that are required for developing phage-based applications for various sectors, including biocontrol, detection and typing. View Full-Text
Keywords: Bacteriophage; Salmonella; biocontrol; comparative genomics; phage diversity Bacteriophage; Salmonella; biocontrol; comparative genomics; phage diversity
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Fong, K.; Tremblay, D.M.; Delaquis, P.; Goodridge, L.; Levesque, R.C.; Moineau, S.; Suttle, C.A.; Wang, S. Diversity and Host Specificity Revealed by Biological Characterization and Whole Genome Sequencing of Bacteriophages Infecting Salmonella enterica. Viruses 2019, 11, 854.

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