Global Genomic Analysis Reveals Spatial Patterns and Temporal Trends of Priority-Antimicrobial Resistance in Salmonellaenterica Isolates from Aquatic Animals

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Antimicrobial resistance (AMR) in Salmonella enterica from aquatic animals represents an emerging food safety and public health concern, yet the global distribution patterns and trends remain insufficiently understood. Here, we performed a global genomic survey of Salmonella from aquatic animals using 2911 genomes collected from 67 countries across six continents between 1974 and 2025. These genomes represented 194 serovars and 364 sequence types. Notably, the dataset exhibited unbalanced geographical sampling, with Asian isolates accounting for 69.98% of all strains, which may limit the generalizability of our global trends. Globally, resistance to WHO-recommended clinically important antimicrobials showed substantial variation among antibiotic classes, with resistance rates for azithromycin (2.10%), cefepime (2.89%), cefotaxime (2.71%), ceftazidime (2.71%), and ceftriaxone (0.62%). Geographical differences were observed, with isolates from Asia exhibiting higher resistance levels, particularly for ciprofloxacin (13.50%) and doxycycline (18.02%). AMR temporal trends differed across geographical regions. A total of 111 acquired ARGs and 10 resistance-associated chromosomal mutations were identified, accompanied by changes in the distribution of resistance determinants. Collectively, this study provides a global genomic perspective on priority AMR in Salmonella from aquatic animals and highlights the importance of integrating aquaculture, environmental, and public health surveillance to monitor and mitigate AMR risks within the One Health framework.

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