Antimicrobial Resistance and Associated Genetic Determinants of Aliivibrio Colonizing the Gastrointestinal Tract of Farmed Atlantic Salmon (Salmo salar L.)

Background/Objectives: Currently, readily available data on antimicrobial resistance in bacteria colonizing farmed Atlantic salmon (Salmo salar L.) are limited. Recent data indicate that the gastrointestinal tract mucosa of adult Atlantic salmon farmed in Tasmania (Australia) is consistently colonized by Aliivibrio species. Aliivibrio and other Vibrionaceae may contribute to gut dysbiosis through overgrowth. We investigated Aliivibrio isolates and other Aliivibrio species to link antimicrobial resistance (AMR) phenotypes with the presence of antimicrobial resistance genes (ARGs). Methods: We performed antimicrobial susceptibility testing on Atlantic salmon bacterial isolates (n = 50). We surveyed ARGs in representative genome-sequenced strains (n = 21) and across the genus Aliivibrio (n = 112 strains) using a range of bioinformatic approaches. Results: Salmon Aliivibrio isolates had high MIC values for multiple antimicrobial drug classes (penams, tetracyclines, sulfonamides, macrolides, and aminoglycosides), including antimicrobials important for aquaculture prophylaxis. The greatest susceptibility was observed for chloramphenicol, oxolinic acid, ciprofloxacin, rifampicin, meropenem, trimethoprim, and trimethoprim–sulfamethoxazole. Provisional analysis suggests that the resistance profile of Aliivibrio isolates matches a core set of predicted ARGs common to the genus Aliivibrio. Among the isolates, plasmids and integrons did not include genes similar to known ARGs. Based on available genome data, strains of several Aliivibrio species carried predicted ARGs on integrons, including genes providing potential resistance to chloramphenicol (cpt, catB), tetracyclines (tetE), sulfonamides (sul2), and trimethoprim (dfrA1). Conclusions: Based on these results, we estimated provisional epidemiological cutoff values for several antimicrobials for Aliivibrio isolates predominant in Atlantic salmon farmed in Tasmania. Furthermore, available data show no evidence that plasmid- or integron-associated ARGs are prevalent and suggest that they are, overall, uncommon in the genus Aliivibrio. The data presented provide a foundation for monitoring AMR in Atlantic salmon gut-associated commensal bacteria.