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

Abstract

andcause 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 fiveandisolates, 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 ofand, recovered from different aquatic sources. Findings from this study revealed large genomic variability across globalpopulations, with a clear distinction in the pan-genome betweenspecies.multi-locus sequence type analysis revealed a wide distribution of sequence types (STs) 656 and 251 in Asia inand, 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, withdemonstrating greater diversity in virulence genes compared with. Country-specific virulence pathways were also noted for several toxins and secretion systems, including,and type III and IV secretion systems. This work provides new insights into the genomic features and relatedness ofspp. 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.