AUTHOR=Bartkova Simona , Leekitcharoenphon Pimlapas , Aarestrup Frank M. , Dalsgaard Inger 

TITLE=Epidemiology of Danish Aeromonas salmonicida subsp. salmonicida in Fish Farms Using Whole Genome Sequencing

JOURNAL=Frontiers in Microbiology

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.02411

DOI=10.3389/fmicb.2017.02411

ISSN=1664-302X

ABSTRACT=<p>Furunculosis, a serious infection caused by the bacterium <italic>Aeromonas salmonicida</italic> subsp. <italic>salmonicida</italic> 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 <italic>A. salmonicida</italic> subsp. <italic>salmonicida</italic> isolates. To obtain this, the genomes of 101 <italic>A. salmonicida</italic> subsp. <italic>salmonicida</italic>, including 99 Danish isolates, one Scottish strain and the type strain NCIMB 1102, were sequenced using the Illumina HiSeq platform. Isolates were <italic>de novo</italic> 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 <italic>A. salmonicida</italic> subsp. <italic>salmonicida</italic> A449 as reference. Bayesian temporal phylogenetic reconstruction suggests that four major introductions of <italic>A. salmonicida</italic> subsp. <italic>salmonicida</italic> 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 <italic>A. salmonicida</italic> subsp. <italic>salmonicida</italic> mostly appeared to be associated with their plasmids and plasmid encoded virulence factors. Nine <italic>A. salmonicida</italic> subsp. <italic>salmonicida</italic> 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 <italic>A. salmonicida</italic> subsp. <italic>salmonicida</italic> population, with implications for vaccine development in efforts to better protect Danish rainbow trout in the future.</p>