Pan-resistome and genomic plasticity analysis of antibiotic resistance in <i>Aeromonas:</i> new vaccine targets for <i>A. caviae, A. veronii</i> and <i>A. hydrophila</i> through reverse vaccinology

Aeromonas species are globally significant pathogens. However, the mechanisms driving their antimicrobial resistance patterns remain unclear. This study addresses the spread of resistance genes in the Aeromonas genus through a large-scale genomic analysis of all complete Aeromonas genomes in the RefSeq database. The emergence of next-generation genomic sequencing enabled the sequencing, assembling and annotation of numerous genomes with a description and characterization of the genomic plasticity and the pan-resistome, through bioinformatics programmes, of each species in the Aeromonas genus, and revealed species-specific patterns of resistance determinants. Leveraging these genomic insights, we applied a reverse vaccinology approach with a subtractive genomic workflow to select novel in silico vaccine targets for the three main pathogens: A. veronii, A. hydrophila and A. caviae. These protein candidates offer a potential alternative to prevent the spread of antibiotic resistance genes. Our findings underscore that continuous genomic surveillance is essential for monitoring established and emerging pathogens. While further in vitro and in vivo validation is pending, this work provides a robust framework for understanding Aeromonas resistance and developing new strategies to protect public and environmental health.