Genomic screening of eight antibiotic-resistant Pseudomonas isolated from rainbow trout (Oncorhynchus mykiss)
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Open aquaculture systems represent a strategic environment for the study of antibiotic resistance dynamics given the interactions between bacteria from humans, animals and the environment. The genomic investigation of eight Pseudomonas isolated from rainbow trout in a previous study demonstrated that non-wild-type and resistance phenotypes to several antibiotics (oxytetracycline, sulphonamides, florfenicol) were predominantly attributable to the presence of related genes (tet(Y), sul2 and floR). Phylogenetic analyses revealed that several the species Pseudomonas iridis harboured these genes on mobile genetic elements, including integrative conjugative elements on the chromosome or plasmids with a high degree of sequence similarity (>99%) between the genetic structures. Furthermore, comparisons between isolates with low and high MIC values to colistin showed mutations amino acid sequences of the PhoP/Q two-component system and a lack of the pmrA/B system. A wide diversity of known lipopolysaccharide-modifying genes involved in colistin resistance were also detected in resistant isolates. This study provided insights into the dynamics of antibiotic resistance in aquaculture systems. It demonstrated the presence of genes located on an integrative conjugative element (ICE) inserted into a chromosome or plasmid in Pseudomonas iridis, which was isolated from healthy rainbow trout in different farms within the same watershed. Our study raises questions about the ability of environmental Pseudomonas bacteria to spread their antibiotic resistance genes to other bacterial species that are of interest in terms of human or animal surveillance
