Mapping Resistance in the Waters: Tackling AMR in the Asian Seabass Supply Chain through Genomic Surveillance

By Asst. Prof. Dr. Jirakrit Saetang and Team 

Editor: Anti Rismayanti, SEAOHUN Regional Program Manager

Amid growing concerns over antimicrobial resistance (AMR) in food systems, the SEAOHUN One Health Research and Training (OHRT) Awards Program offered an invaluable opportunity to explore the presence of AMR genes within aquaculture environments. Our team, led by Asst. Prof. Dr. Jirakrit Saetang from Prince of Songkla University, embarked on a project titled "Investigation of antimicrobial resistance (AMR) genes in Asian seabass throughout the supply chain in Southern Thailand by Nanopore sequencing approach." This initiative marked a significant step toward understanding how AMR might travel from aquatic farms to consumer tables, with implications for food safety, public health, and environmental sustainability.

Implementation Experience

Our implementation journey began with the collection of samples from various points along the supply chain—including aquaculture farms, container surfaces, and local markets—located in Songkhla, Thailand. Water was sampled from both inside and outside cage farms, while containers were swabbed, and fish were procured directly from markets. Samples were processed using Oxford Nanopore sequencing, a real-time DNA sequencing technology that allowed us to assess both resistome and microbiome profiles in each environment.

While the technical process progressed efficiently, our field operations were met with logistical hurdles, such as coordinating multiple sampling sites and managing sample quality across different environmental matrices. However, strong collaboration among team members from various disciplines and institutions helped us overcome these obstacles. The sequencing results yielded a rich dataset of over 12 million reads, capturing bacterial diversity and AMR gene patterns across environments.

Enhancement of One Health Knowledge and Skills

The project significantly enriched the technical and practical understanding of One Health among team members. We advanced our laboratory skills in high-throughput DNA extraction and nanopore sequencing, and gained fluency in bioinformatics tools such as Kraken2, Phyloseq, and the Resistance Gene Identifier. More importantly, the project nurtured crucial soft skills such as stakeholder communication, particularly when translating genomic concepts into practical implications for farmers and local vendors. This dual capacity in science and engagement is essential for implementing impactful One Health solutions.

Improving One Health Education and Practice

As faculty at OHUN member universities, our team is already leveraging the knowledge gained to enrich academic curricula. Modules on AMR monitoring and microbial sequencing are being developed, integrating both theory and field practice. Students will benefit from exposure to real-world applications of genomic surveillance, enhancing their readiness to tackle health threats that cross human, animal, and environmental domains. This approach not only improves knowledge transfer but also promotes a holistic mindset critical to solving One Health challenges.

Results and Insights

Our results revealed critical insights into bacterial diversity and ARG (antimicrobial resistance gene) distribution. Synechococcus dominated the water microbiome, reflecting its role as a marine primary producer. Vibrio species appeared more abundantly inside fish cages at some sites, indicating potential health risks due to poor farming conditions. Containers exhibited different microbial profiles, including heat-tolerant Kocuria species, possibly introduced during storage and transportation.

Fish samples presented a concerning profile, with bacterial genera such as Acinetobacter, Aeromonas, and Shewanella being consistently present. These genera include species that are not only pathogenic to fish but also resistant to multiple antibiotics, posing threats to food safety and human health. Notably, pathogenic species such as Acinetobacter johnsonii and Aeromonas salmonicida were detected alongside spoilage-related Shewanella baltica.

The resistome analysis identified key ARGs such as rsmA, MOX-13, OXA-436, and rpsL. These genes confer resistance to commonly used antibiotics, including fluoroquinolones, cephalosporins, and streptomycin. The rsmA gene—present in containers and fish—highlighted the potential transfer of resistance during storage and handling. The detection of the rpsL gene in water samples, a marker for streptomycin resistance, underscored environmental contamination possibly linked to past antibiotic usage. These findings emphasize the interconnected nature of AMR across sectors.

Public Awareness and Stakeholder Engagement

Beyond laboratory results, the project included a strategic social media campaign aimed at raising AMR awareness among farmers, vendors, and the broader public. Although some components were delayed, initial content creation, including infographic design and message development, is in progress. The campaign will be rolled out via Facebook, Instagram, and relevant Thai governmental websites beginning in November 2024.

Stakeholder engagement was integral throughout the project. Farmers were informed about the implications of antibiotic overuse and introduced to alternatives such as probiotics and vaccines. These interactions helped build trust and empowered farmers to explore sustainable aquaculture practices. Additionally, fact sheets summarizing our findings are being prepared for dissemination to national agencies overseeing food safety and AMR control.

Anticipated Impact and Future Directions

We anticipate that our findings will influence AMR surveillance policy and aquaculture management practices in Thailand. With data archived in the NCBI Sequence Read Archive and a manuscript in preparation for Food Control, the research will contribute to the global AMR discourse. Over the next six months, our outreach activities will expand, with the aim of sustaining behavioral change among farmers and promoting policy-level dialogue.

We are also exploring the expansion of surveillance systems for continuous monitoring, supported by additional funding proposals. Such systems could include routine testing at fish markets and processing centers, supported by genomic dashboards that inform local AMR trends.

Contributing to the Advancement of One Health

This project exemplifies a robust One Health approach, bridging environmental science, veterinary pathology, food safety, and public engagement. It sets a precedent for how portable sequencing tools and cross-sectoral partnerships can address complex health threats. By fostering awareness, generating actionable data, and advocating sustainable practices, we are actively advancing the One Health agenda in Thailand and potentially, the broader Southeast Asian region.

Insights and Lessons Learned

Key lessons emerged throughout the project. Early and clear communication with stakeholders was crucial—simplifying scientific language using relatable analogies helped drive the message home. Preparing the team with field training ahead of sample collection optimized our workflow and minimized errors. We also learned the importance of robust data curation; even small misclassifications in ARG identification could lead to misinformed conclusions.

Conclusion

The SEAOHUN OHRT Awards Program has empowered our team to conduct meaningful research on AMR, bridging science and society in the process. Our results offer a foundation for long-term surveillance and sustainable aquaculture, while also enriching One Health education and collaborative practices. As we continue to share findings and expand our efforts, we aim to inspire other researchers, policymakers, and practitioners to join the fight against antimicrobial resistance—one genome at a time.

Team Leader: Asst. Prof. Dr. Jirakrit Saetang, Prince of Songkla University

Team Members:

• Prof. Dr. Soottawat Benjakul, Prince of Songkla University

• Asst. Prof. Dr. Matsapume Detcharoen, Prince of Songkla University

• Asst. Prof. Dr. Chonticha Romyasamit, Walailak University

• Asst. Prof. Dr. Watcharapol Suyapoh, Prince of Songkla University