Are the genomes of motile Aeromonas species from the aquatic environment shaped by local geography and host species?

Aeromonas dhakensis and Aeromonas hydrophila cause significant economic losses within the global aquaculture sector, affecting numerous farmed fish species and posing a zoonotic threat to human health. In this study, we sequenced, assembled and analysed the genomes of seven and five A. dhakensis and A. hydrophila isolates, respectively, recovered from disease outbreaks in various fish hosts across Southeast Asia using a hybrid sequencing approach with Illumina and Oxford Nanopore technologies. To assess the relatedness of our isolates with those from the global aquatic environment, with particular reference to aquaculture-relevant systems, and compare their resistome and virulome profiles, we also conducted comparative genomic analysis with an additional 57 publicly available genomes of A. dhakensis and A. hydrophila , recovered from different aquatic sources. Findings from this study revealed large genomic variability across global Aeromonas populations, with a clear distinction in the pan-genome between Aeromonas species. In silico multi-locus sequence type analysis revealed a wide distribution of sequence types (STs) 656 and 251 in Asia in A. dhakensis and A. hydrophila , respectively, although the novel STs detected in Indonesia and the Philippines suggest local adaptation of populations circulating in these countries. Analysis of mobile genetic elements revealed plasmids, insertion sequences and genomic islands to be country- or host-specific. Exploration of resistome data revealed a high prevalence of multidrug resistance across Southeast Asia, with genomes frequently carrying resistance genes against antibiotic classes commonly used across the aquaculture sector, including potentiated sulphonamides and tetracyclines. However, several antimicrobial resistance genes were found to be country- or host-specific, suggesting local adaptation to anthropogenic or environmental conditions within specific regions. A diverse repertoire of virulence genes was also detected in this study, with A. hydrophila demonstrating greater diversity in virulence genes compared with A. dhakensis . Country-specific virulence pathways were also noted for several toxins and secretion systems, including aerA/act , rtx and type III and IV secretion systems. This work provides new insights into the genomic features and relatedness of Aeromonas spp. circulating within aquaculture systems in Southeast Asia. Further, findings from comparative genomic analysis highlight the influence of geographical or host pressures on the molecular drivers of antimicrobial resistance and pathogenicity, directly impacting animal health and aquaculture production.