Comparative genomic characterization of publicly available human- and food-associated Aeromonas genomes from diverse countries

Aeromonas spp. are emerging and neglected human pathogens widely distributed in nature. Despite their medical importance, the genomic characteristics of this genus remain incompletely understood. This study screened A. hydrophila (n = 63), A. veronii (n = 236), A. dhakensis (n = 78), and A. salmonicida (n = 13) genomes from strains isolated from human and food sources across 19 countries over a 42-year period for antimicrobial resistance, stress, and virulence genes, as well as plasmid replicons. Their genetic relatedness was assessed by searching single-nucleotide polymorphism (SNP) clusters, multilocus sequence typing (MLST), core-genome MLST (cgMLST), and fragmented-genome analyses. A total of 123 genes encoding resistance to 13 antimicrobial classes and 16 genes associated with heavy-metal tolerance and resistance to heat and disinfectants were observed. Six plasmid replicons were detected in 19 genomes. A total of 245 virulence genes associated with adhesion, secretion systems, and toxins were identified. All phylogenetic analyses suggested high intraspecies diversity, regardless of isolation country, year, or source. In conclusion, the high diversity and frequency of clinically important antimicrobial resistance and virulence genes carried by genetically diverse strains of clinically and environmentally relevant Aeromonas species reinforce the potential hazard of infections caused by these pathogens and the need for more effective surveillance by public health authorities.