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

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.

Comparative Study on A Novel Pathogen of European Seabass. Diversity of Aeromonas veronii in the Aegean Sea

“…Divergence among A. veronii seabass isolates were also at least one order of magnitude higher than the ones reported in A. salmonicida subsp. salmonicida isolated from fresh and seawater farms of trout in Denmark which had a time gap of isolation of approximately 30 years [30].…”

“…Single nucleotide polymorphisms (SNPs) analysis was done according to [30]. Briefly, SNPs were determined using CSI phylogeny [31,32] available on the CGE ().…”

Role of Bacterial Secretion Systems and Effector Proteins – Insight into the Pathogenicity Mechanisms in Aeromonas

“…(Sha et al, 2007) Putative serine/threonine kinase. (Dacanay et al, 2006;Menanteau--Ledouble & El-Matbouli, 2016;Bartkova et al, 2017) Disturbs the normal distribution of actin in the host cell. (Groves et al, 2010) ati2 T3SS Suspected of having inositol polyphosphate phosphatase activity.…”

Comparison of the Multiple Platforms to Identify Various Aeromonas Species

“…With the development of biotechnology, multiplex-PCR is also commonly used for Aeromonas identification (Del Cerro et al, 2002 ; LaFrentz et al, 2019 ). Whole-genome sequencing technology has been widely used in various fields to accurately identify bacterial species by comparing the whole-genome sequences it generates; thus, this technique has become the reference method for bacterial species identification (Jamal et al, 2014 ; Hughes et al, 2016 ; Bartkova et al, 2017 ). MLPA typing is used to identify the characteristics of microbial isolates.…”