Phylogenetic analysis of the fish pathogen Aeromonas salmonicida underlines the dichotomy between European and Canadian strains for the salmonicida subspecies

The Gram-negative bacterium Aeromonas salmonicida, which belongs to the Gammaproteobacteria class, has a taxonomy containing five official subspecies (pectinolytica, masoucida, achromogenes, smithia and salmonicida; Dallaire-Dufresne et al. 2014). There are also three strains from India (Y577, Y47 and Y567; Vincent et al. 2016a), which have an unclear taxonomy and no subspecies assignment yet. This bacterium is of veterinary importance as many taxa belonging to the different subspecies are known to infect fish (Burr & Frey 2007; Austin & Austin 2012), thus causing important livestock losses worldwide (Dallaire-Dufresne et al. 2014). The most studied subspecies of this bacterium is salmonicida, which is sometimes qualified as ‘typical’, and is well known to cause furunculosis, a fish disease mainly affecting salmonids (Austin & Austin 2012). The other psychrophilic subspecies are qualified as ‘atypical’ and infect a wide range of hosts (Dallaire-Dufresne et al. 2014). Early in the research field of A. salmonicida subsp. salmonicida, one study reported a genetic grouping of this bacterium based on geographical regions (Finland, Denmark, Sweden, Norway and Canada) using ribotyping and random amplified polymorphic DNA (RAPD) profiling (H€anninen, Ridell & Hirvel€a-Koski 1995). Many other studies reported that A. salmonicida subsp. salmonicida isolates are genetically highly homogeneous with a clonal population structure (Belland & Trust 1988; McCormick, Stevenson & MacInnes 1990; Umelo & Trust 1998; Garc ıa et al. 2000; O’hIci, Olivier & Powell 2000). However, these studies were based on low-resolution approaches, making it perilous to conclude on the genetic diversity of A. salmonicida subsp. salmonicida strains, which are evolutionarily close. With the advances in sequencing technologies (Vincent et al. 2016c), some studies found differences in the mobilome between European and Canadian strains. For example, European strains have a greater tendency to lack small plasmids pAsa3 and pAsal1 compared to Canadian isolates (Att er e et al. 2015). However, one of the strongest discrepancies between the European and the Canadian strains is the genomic island AsaGEI. Many variants of this genomic island were reported (AsaGEI1a, 1b, 2a, 2b and finally 2c; Emond-Rheault et al. 2015a,b; Long et al. 2016). Correspondence S J Charette, Institut de Biologie Int egrative et des Syst emes (IBIS), Pavillon Charles-Eug ene-Marchand, 1030 avenue de la M edecine, Universit e Laval, Quebec City, QC G1V 0A6, Canada (e-mail: steve.charette@bcm.ulaval.ca)