Variants of a genomic island in Aeromonas salmonicida subsp. salmonicida link isolates with their geographical origins

Jean-Guillaume Emond-Rheault; Antony T Vincent; Mélanie V Trudel; Francis Brochu; Brian Boyle; Katherine H Tanaka; Sabrina A Attéré; Éric Jubinville; Thomas P Loch; Andrew D Winters; Mohamed Faisal; Michel Frenette; Nicolas Derome; Steve J Charette

doi:10.1016/j.vetmic.2014.11.014

Variants of a genomic island in Aeromonas salmonicida subsp. salmonicida link isolates with their geographical origins

Vet Microbiol. 2015 Jan 30;175(1):68-76. doi: 10.1016/j.vetmic.2014.11.014. Epub 2014 Nov 22.

Affiliations

¹ 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.
² 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.
³ Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada.
⁴ Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA.
⁵ 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.
⁶ 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.
⁷ 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.

PMID: 25480167
DOI: 10.1016/j.vetmic.2014.11.014

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.

Keywords: Aeromonas salmonicida; Fish pathogen; Furunculosis; Genomic island; Genomics/functional genomics/comparative genomics; Geographical distribution.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Aeromonas salmonicida / genetics*
Animals
Base Sequence
Chromosomes, Bacterial / genetics*
Fish Diseases / microbiology*
Fishes
Furunculosis / microbiology
Genetic Variation*
Genomic Islands / genetics*
Genomics
Geography
Gram-Negative Bacterial Infections / microbiology
Gram-Negative Bacterial Infections / veterinary*
Molecular Sequence Data
Mutagenesis, Insertional
Sequence Analysis, DNA
Species Specificity

Associated data

GENBANK/KJ626178
GENBANK/KJ626179
GENBANK/KJ626180