Edwardsiella ictaluri continues to pose a significant risk to the health and production of striped catfish (Pangasianodon hypophthalmus) in Vietnam. Whilst recent advances in genomic sequencing provide an insight into the global genomic diversity of this important fish pathogen, genome-wide analysis of Vietnamese isolates recovered over time is lacking. In this study, we used a whole-genome sequencing approach to compare the genomes of 31 E. ictaluri isolates recovered over a 20-year period (2001–2021) and performed comparative genomic analysis to explore temporal changes in genome diversity, population structure and mechanisms driving pathogenesis and antimicrobial resistance. Our findings revealed an open pan-genome with 4148 genes and a core genome (3 060 genes) accounting for over two-thirds of the genome. Moreover, we found the genomes sequenced to classify into two distinct lineages and estimated the ancestral origin of these lineages within Vietnam to date back to the 1950s. Plasmids were highly prevalent in Vietnamese E. ictaluri, with isolates harbouring up to four plasmids within their genome. Further, a diverse mobilome was observed with nine different plasmid types detected across the genome collection. Exploration of putative plasmids revealed a diverse set of antimicrobial resistance genes (ARGs) against key antibiotics used in Vietnamese aquaculture and virulence genes associated with protein secretion systems. Correlation analysis revealed the total number of ARGs detected in genomes to increase with isolate recovery time. Whilst the number of virulence genes remained relatively stable, temporal variation was noted in several virulence factors related to motility and immune system modulation. Findings from this study highlight the need for continued genomic surveillance to monitor changes in antimicrobial resistance and pathogenesis, to help inform the development of disease control and management strategies.

(1) Background: Antibiotic (AB) usage in food animals is a significant contributor to antimicrobial resistance (AMR). Vaccination can reduce the over-use of AB treatment. Little is known about farmers’ attitudes and beliefs about AB and vaccine usage in developing countries, especially in aquaculture. (2) Methods: We used the necessity/concerns framework to guide our research, where vaccine hesitancy is viewed as a function of the perceived necessity versus the perceived concerns about treatment. We measured disease and treatment perceptions in 400 Vietnamese farmers of Pangasius catfish, specifically regarding (a) chemical treatment of water, (b) antibiotic usage, and (c) vaccination of fish. (3) Results: Although farmers’ concerns about AB usage outweighed necessity beliefs, 86.5% reported having used ABs on their farm. Knowledge and attitudes towards vaccination were positive, with views of its necessity outweighing concerns. However, if available, only 67.6% said they would definitely use vaccines in the future. Farmers were more likely to use vaccines if they reported having fewer problems with fish disease, felt that any concerns about vaccines were outweighed by their perceived benefits, had less mistrust of vaccination, and had fewer concerns about commercial profiteering. (4) Conclusion: Interventions that highlight concerns about continued antibiotic use, reduce concerns, and mistrust and increase the perceived necessity of vaccines combined with greater availability of vaccines may be the most effective way of overcoming vaccine hesitancy and increase appropriate use of vaccines by Vietnamese fish farmers.

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.