Genomic screening of eight atypical antibiotic-resistant Pseudomonas isolated from rainbow trout (Oncorhynchus mykiss)

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 multiple species of Pseudomonas harboured these genes on mobile genetic elements, including integrative conjugative elements or plasmids with a high degree of sequence similarity (>99%) between the genetic structures. Furthermore, this study identified an arnCADTEF operon in the three colistin-resistant isolates, which could explain the observed phenotypes with moderate to high minimum inhibitory concentrations (ranging from 16 µg/mL to more than 1,024 µg/mL). This study provided insights into the putative antibiotic resistance dynamics in aquaculture systems, demonstrating the presence of shared genes in diverse mobile genetic elements (plasmid, integrative conjugative elements) within the Pseudomonas genus, which were harboured by rainbow trout reared in different farms within the same watershed. Given the limited number of isolates analysed, our study raises questions about the frequency of these genetic events in these environments.