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Levesque, Roger

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Levesque

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Roger

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Université Laval. Département de microbiologie-infectiologie et d'immunologie

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ncf10164869

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  • PublicationAccès libre
    Salmonella enterica prophage sequence profiles reflect genome diversity and can be used for high discrimination subtyping
    (Frontiers Media S.A., 2018-05-04) Mottawea, Walid; Moineau, Sylvain; Kukavica-Ibrulj, Iréna; Dupras, Andrée Ann; Hamel, Jérémie; Usongo, Valentine; Bekal, Sadjia; Jeukens, Julie; Duceppe, Marc-Oliver.; Emond Rheault, Jean-Guillaume; Levesque, Roger; Boyle, Brian; Freschi, Luca; Gill, Alexander; Burnett, Elton; Franz, Eelco; Arya, Gitanjali; Weadge, Joel T.; Gruenheid, Samantha; Wiedmann, Martin; Huang, Hongsheng; Daigle, France; Goodridge, Lawrence; Ogunremi, Dele
    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.
  • PublicationAccès libre
    Diversity and host specificity revealed by biological characterization and whole genome sequencing of bacteriophages infecting salmonella enterica
    (MDPI, 2019-09-14) Fong, Karen; Tremblay, Denise; Moineau, Sylvain; Delaquis, Pascal; Levesque, Roger; Goodridge, Lawrence; Suttle, Curtis Arnold; Wang, Siyun
    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.
  • PublicationAccès libre
    A syst-OMICS approach to ensuring food safety and reducing the economic burden of salmonellosis
    (Frontiers Media S.A., 2017-06-02) Tremblay, Denise; Groleau, Gisèle.; Loignon, Stéphanie; Vincent, Caroline; Moineau, Sylvain; Colavecchio, Anna; Kukavica-Ibrulj, Iréna; Barrere, Virginie; Fliss, Ismaïl; Cadieux, Brigitte; Bekal, Sadjia; Arya, Gitanjali; Dewar, Ken; Fournier, Éric; Berry, Chrystal; Jeukens, Julie; Burnett, Elton; Emond Rheault, Jean-Guillaume; Levesque, Roger; Chapin, Travis K.; Dupont, Marie-Josée; Crouse, Alanna; Boyle, Brian; Daigle, France; Freschi, Luca; Danyluk, Michelle D.; Delaquis, Pascal J.; Doualla-Bell, Florence; Fong, Karen; Franz, Eelco; Garduno, Rafael; Gill, Alexander; Gruenheid, Samantha; Harris, Linda J.; Huang, Carol B.; Huang, Hongsheng; Johnson, Roger; Joly, Yann; Kerhoas, Maud; Kong, Nguyet; Larivière, Line; Malo, Danielle; Mottawea, Walid; Mukhopadhyay, Kakali; Nadon, Céline; Nash, John; Ngueng Feze, Ida; Ogunremi, Dele; Perets, Ann; Pilar, Ana V.; Reimer, Aleisha R.; Robertson, James; Rohde, John; Sanderson, Kenneth E.; Song, Lingqiao; Stephan, Roger; Tamber, Sandeep; Thomassin, Paul J.; Usongo, Valentine; Wang, Siyun; Weadge, Joel T.; Wiedmann, Martin; Wijnands, Lucas; Wilson, Emily D.; Wittum, Thomas; Yoshida, Catherine; Yousfi, Khadija; Zhu, Lei; Weimer, Bart C.; Goodridge, Lawrence; Cavestri, Camille
    The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS), at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment. The ultimate goals are to understand how Salmonella evolves over time, improve the accuracy of diagnostic methods, develop control methods in the field, and identify prognostic markers for evidence-based decisions in epidemiology and surveillance.