Abstract
Furunculosis, a serious infection caused by the bacterium Aeromonas salmonicida subsp. salmonicida is common in sea-reared rainbow trout production in Denmark. Developing an effective control strategy requires knowledge of the epidemiology, as well as the genomic and virulent variability of the Danish A. salmonicida subsp. salmonicida isolates. To obtain this, the genomes of 101 A. salmonicida subsp. salmonicida, including 99 Danish isolates, one Scottish strain and the type strain NCIMB 1102, were sequenced using the Illumina HiSeq platform. Isolates were de novo assembled, examined for presence of plasmids, virulence and iron acquisition proteins, genomic islands, and antibiotic resistance genes. Single Nucleotide Polymorphisms were aligned and subjected to Bayesian temporal phylogenetic and maximum likelihood tree reconstruction using the published genome of A. salmonicida subsp. salmonicida A449 as reference. Bayesian temporal phylogenetic reconstruction suggests that four major introductions of A. salmonicida subsp. salmonicida into Denmark have occurred. The introductions correlate with the freshwater and subsequent seawater expansion of rainbow trout production. Initial transmission of the bacterium could have been from seawater to freshwater or vice versa, and most minor clades include a mixture of strains from different fresh- and seawater farms. Genomic variation of A. salmonicida subsp. salmonicida mostly appeared to be associated with their plasmids and plasmid encoded virulence factors. Nine A. salmonicida subsp. salmonicida isolates harbored worldwide known antibiotic resistance genes against several antibiotics and there is an indication that 33% of the isolates contained the genomic island AsaGEI1b. These findings not only support the usefulness of whole genome sequencing for genetic studies of homogeneous bacteria in general, but provide novel information about the Danish A. salmonicida subsp. salmonicida population, with implications for vaccine development in efforts to better protect Danish rainbow trout in the future.
Highlights
Aeromonas salmonicida subsp. salmonicida, the causative agent of a serious infection furunculosis, was first isolated by Emmerich and Weibel (1894) at a German freshwater brown trout hatchery
The two Danish A. salmonicida subsp. salmonicida (Mj2 1990 and Sd8 1992), which were the only isolates from Denmark that were isolated from brown trout instead of rainbow trout, had an average difference of 50 and 42 SNPs respectively when compared to the rest of the isolate collection
The two Danish A. salmonicida subsp. salmonicida isolated from brown trout (Mj2 1990 and Sd8 1992) and the type strain NCIMB 1102 from Atlantic salmon grouped together with Danish A. salmonicida subsp. salmonicida from rainbow trout in one of the four major clades (Figure 1) and only have an average difference of 41, 50, and 52 SNPs, which challenges the theory of A. salmonicida subsp. salmonicida genome adapting to the environment of their specific hosts species (Reith et al, 2008)
Summary
Aeromonas salmonicida subsp. salmonicida, the causative agent of a serious infection furunculosis, was first isolated by Emmerich and Weibel (1894) at a German freshwater brown trout hatchery. In the late 1970s, production was extended to seawater and dry pellet feed was introduced instead of the common wet feed consisting of herring, whiting, sand-eels and other marine fish not used for human consumption (Christensen, 1980) Both actions increased the growth of the Danish rainbow trout production even further. Despite fish being vaccinated before transfer from freshwater to seawater farms, furunculosis has occurred repeatedly during situations with elevated water temperatures (Larsen and Mellergaard, 1981; Dalsgaard and Madsen, 2000; Pedersen et al, 2008) This situation, along with previous research, has led to the belief that A. salmonicida subsp. Verifying this would be critical for developing an effective prevention strategy against furunculosis
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