title: Variants of a genomic island in Aeromonas salmonicida subsp. salmonicida link isolates with their geographical origins.
abstract: Aeromonas salmonicida subsp. salmonicida is a fish pathogen. Analysis of its genomic characteristics is required to determine the worldwide distribution of the various populations of this bacterium. Genomic alignments between the 01-B526 pathogenic strain and the A449 reference strain have revealed a 51-kb chromosomal insertion in 01-B526. This insertion (AsaGEI1a) has been identified as a new genomic island (GEI) bearing prophage genes. PCR assays were used to detect this GEI in a collection of 139 A. salmonicida subsp. salmonicida isolates. Three forms of this GEI (AsaGEI1a, AsaGEI1b, AsaGEI2a) are now known based on this analysis and the sequencing of the genomes of seven additional isolates. A new prophage (prophage 3) associated with AsaGEI2a was also discovered. Each GEI appeared to be strongly associated with a specific geographic region. AsaGEI1a and AsaGEI2a were exclusively found in North American isolates, except for one European isolate bearing AsaGEI2a. The majority of the isolates bearing AsaGEI1b or no GEI were from Europe. Prophage 3 has also a particular geographic distribution and was found only in North American isolates. We demonstrated that A. salmonicida subsp. salmonicida possesses unsuspected elements of genomic heterogeneity that could be used as indicators to determine the geographic origins of isolates of this bacterium.
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC, G1V 4G5, Canada.
authors.forename: Jean-Guillaume
authors.initials: JG
authors.lastname: Emond-Rheault
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC, G1V 4G5, Canada.
authors.forename: Antony T
authors.initials: AT
authors.lastname: Vincent
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC, G1V 4G5, Canada.
authors.forename: Mélanie V
authors.initials: MV
authors.lastname: Trudel
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada; Département de biologie, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.
authors.forename: Francis
authors.initials: F
authors.lastname: Brochu
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada.
authors.forename: Brian
authors.initials: B
authors.lastname: Boyle
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC, G1V 4G5, Canada.
authors.forename: Katherine H
authors.initials: KH
authors.lastname: Tanaka
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC, G1V 4G5, Canada.
authors.forename: Sabrina A
authors.initials: SA
authors.lastname: Attéré
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC, G1V 4G5, Canada.
authors.forename: Éric
authors.initials: É
authors.lastname: Jubinville
authors.affiliation: Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA.
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Loch
authors.affiliation: Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Winters
authors.affiliation: Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI 48824, USA.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Faisal
authors.affiliation: Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada; Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, Canada G1V 0A6.
authors.forename: Michel
authors.initials: M
authors.lastname: Frenette
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada; Département de biologie, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Derome
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC, G1V 4G5, Canada. Electronic address: steve.charette@bcm.ulaval.ca.
authors.forename: Steve J
authors.initials: SJ
authors.lastname: Charette
mesh_terms: D048409:Aeromonas salmonicida / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D002876:Chromosomes, Bacterial / Q000235:genetics*; D005393:Fish Diseases / Q000382:microbiology*; D005399:Fishes; D005667:Furunculosis / Q000382:microbiology; D014644:Genetic Variation; D044404:Genomic Islands / Q000235:genetics*; D023281:Genomics; D005843:Geography; D016905:Gram-Negative Bacterial Infections / Q000382:microbiology / Q000662:veterinary*; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D017422:Sequence Analysis, DNA; D013045:Species Specificity
keywords: Aeromonas salmonicida; Fish pathogen; Furunculosis; Genomic island; Genomics/functional genomics/comparative genomics; Geographical distribution