Furunculosis, caused by Aeromonas salmonicida, poses a significant threat to both salmonid and non-salmonid fish in diverse aquatic environments. This study explores the genomic intricacies of re-emergent A. salmonicida outbreaks in Atlantic salmon (Salmo salar). Previous clinical cases have exhibited pathological characteristics, such as periorbital hemorrhages and gastrointestinal abnormalities. Genomic sequencing of three Chilean isolates (ASA04, ASA05, and CIBA_5017) and 25 previously described genomes determined the pan-genome, phylogenomics, insertion sequences, and restriction-modification systems. Unique gene families have contributed to an improved understanding of the psychrophilic and mesophilic clades, while phylogenomic analysis has been used to identify mesophilic and psychrophilic strains, thereby further differentiating between typical and atypical psychrophilic isolates. Diverse insertion sequences and restriction-modification patterns have highlighted genomic structural differences and virulence factor predictions can emphasize exotoxin disparities, especially between psychrophilic and mesophilic strains. Thus, a novel plasmid was characterized, which emphasized the role of plasmids in virulence and antibiotic resistance. The analysis of antibiotic resistance factors revealed resistance against various drug classes in Chilean strains. Overall, this study elucidates the genomic dynamics of re-emergent A. salmonicida and provides novel insights into their virulence, antibiotic resistance, and population structure. However, rigorous monitoring and control in aquaculture remain crucial to mitigate the spread of antibiotic resistance.

The migratory life history of anadromous salmonids requires successful migration between nursery, feeding and spawning habitats. Smoltification is the major transformation anadromous salmonids undergo before migration to feeding areas and prepares juvenile fish for downstream migration and entry to seawater. We reviewed the effects of climate change on smolt ecology from growth of juveniles in freshwater to early post-smolts in sea. Shift in the suitable thermal conditions by climate change is causing Atlantic salmon to expand their range northwards, while in the southern edge of their distribution populations struggle with high temperatures and occasional droughts. Climatic conditions, particularly warmer temperatures, are affecting growth during freshwater phase in the river. Better growth in the northern latitudes leads to earlier smoltification. Thermal refuges, the areas of cooler water in the river, are especially important for salmonids impacted by climate change. Restoring and maintaining connectivity and suitable diverse mosaic habitat in rivers are important for survival and growth throughout the range. The start of the smolt migration has shifted earlier as a response to increasing water temperatures, which has led to concerns of mismatch with optimal conditions for post-smolts in the sea decreasing their survival. A wide smolt window allowing all migrating phenotypes from early to late migrant’s safe access to sea is important in changing environmental conditions. This is true also for regulated rivers, where flow regulation practices cause selection pressures on migrating salmonid phenotypes. Life history in freshwater affects also marine survival, and there is a need for better collaboration across life stages and habitats among researchers and managers to boost the smolt production in rivers.

Maintaining the high overall health of farmed animals is a central tenant of their well-being and care. Intense animal crowding in aquaculture promotes animal especially in the absence of straightforward methods for monitoring their health. Here, we used bacterial 16S ribosomal RNA gene sequencing to measure population dynamics occurring during P. salmonis outbreaks. Our findings revealed a complex bacterial community consisting of a previously undescribed core pathobiome. Notably, we detected Aliivibrio wodanis and Tenacibaculum dicentrarchi on the skin ulcers of salmon infected with P. salmonis, while Vibrio spp. were enriched on infected gills. The prevalence of these co-occurring networks indicates the influence that coinfection plays in P. salmonis pathogenicity.