Genomic Surveillance as a Catalyst for Change: Advancing One Health through AMR Monitoring in Indonesia

By Dr. med. vet. Hadri Latif, DVM, MSi and Team

Editor: Anti Rismayanti, SEAOHUN Regional Program Manager 

Antimicrobial resistance (AMR) continues to pose a grave threat to global health, undermining decades of progress in the treatment of infectious diseases and threatening food security, public safety, and economic stability. In Southeast Asia, where densely populated regions coexist with expansive animal farming operations, the challenge becomes even more acute. Indonesia, as a leading poultry producer, is particularly vulnerable.

To respond proactively, the project “Genomic National Surveillance of Antimicrobial Resistance on Broilers Poultry Sector in Indonesia” was implemented under the SEAOHUN OHRT Awards Program. Led by Dr. Hadri Latif and his team at IPB University in close collaboration with the Ministry of Agriculture, the project delivered the country’s first comprehensive genomic analysis of Escherichia coli from broiler chickens—specifically those producing Extended-Spectrum Beta-Lactamase (ESBL-Ec), a major contributor to multidrug resistance (MDR). Through this initiative, Indonesia has not only improved its surveillance capacity but also informed key policy dialogues on AMR control, aligning itself with WHO’s Tricycle Surveillance framework.

Implementation Experience

Over the course of five months, our team carried out a meticulously planned project that spanned sample validation, genome sequencing, and bioinformatics analysis. A total of 120 archived ESBL-Ec isolates collected from eight regional Disease Investigation Centers (DICs) in 2023 were processed, and 113 high-quality isolates were analyzed. The project employed advanced techniques such as the MinION Oxford Nanopore sequencing platform and AMRFinderPlus to map the resistance genes across isolates.

The results were eye-opening: we detected 1,540 antibiotic resistance genes (ARGs) distributed among 71 gene types across multiple antibiotic classes. The presence of blaCTX-M-55, aac(3)-IId, lnu(F), and sul2 genes in more than 70% of the isolates raised urgent red flags. These genes were particularly concentrated in isolates from Medan and Denpasar—regions with intensive poultry farming—highlighting their role as potential AMR hotspots.

The findings contributed directly to the Monitoring and Evaluation (M&E) session of Indonesia’s National Action Plan on AMR (NAP-AMR) 2020–2024, held on September 3, 2024, in Jakarta. Our research findings were disseminated to more than 30 representatives from relevant ministries and organizations, reinforcing the integration of science into national AMR strategies.

Enhancement of One Health Knowledge and Skills

The project offered a powerful platform for skill enhancement and cross-sector learning. For researchers and students from IPB University, the project became a real-world laboratory for applying theoretical knowledge of One Health to practical challenges. They honed competencies in pathogen genomics, bioinformatics using Linux systems, and data analysis—skills increasingly essential in today’s health surveillance landscape.

Beyond technical skills, the project strengthened soft skills such as teamwork, scientific communication, and stakeholder engagement. The team’s interaction with ministry officials during dissemination events enabled them to refine their ability to translate scientific data into actionable recommendations, a crucial skill for any One Health practitioner.

For the government partners, the experience deepened their capacity to interpret genomic data in surveillance and informed their policy development processes. The collaboration between academia and government institutions fostered a mutual understanding that One Health success relies on equal participation and open communication between all sectors.

Improving One Health Education and Practice

As a faculty member at IPB University, Dr. Latif and his colleagues have already begun to integrate the findings from this project into their academic programming. The resistance gene profiles, sequencing workflows, and real-time bioinformatics applications are now used as practical case studies in epidemiology and molecular microbiology courses. Future veterinary professionals are being trained to think beyond phenotypic data and consider genetic markers of resistance—preparing them to respond proactively to zoonotic threats.

At the governmental level, the Ministry of Agriculture is using the project’s findings to inform its policy proposals for the next phase of the NAP-AMR (2025–2029). In particular, the surveillance data supports the recommendation to include genomic-based AMR indicators in the upcoming RPJMN (National Medium-Term Development Plan), advancing AMR policy planning at the national scale.

Anticipated Impact on Target Groups

Looking forward, this project is expected to yield long-term benefits for multiple sectors. The poultry industry stands to gain from the identification of ARG hotspots, allowing producers to modify antibiotic usage, enhance biosecurity, and adopt better veterinary practices. Veterinarians will be able to rely on genomic evidence when making treatment decisions, reducing empirical use of broad-spectrum antibiotics.

For researchers and policymakers, this surveillance framework offers a scalable model that can be replicated across livestock sectors or even in aquatic farming. Educational institutions can continue to use project data and methodologies in student training, thereby cultivating a new generation of One Health professionals equipped to lead in surveillance, diagnostics, and advocacy.

Contributing to the Advancement of One Health

By adopting a multisectoral and interdisciplinary approach, this project serves as a living example of the One Health paradigm in action. It tackled AMR by linking animal health, environmental surveillance, and human health outcomes. The collaborative structure—combining scientific research, government policy, and education—paved the way for more holistic and sustainable AMR control strategies in Indonesia.

Moreover, the alignment with international frameworks such as WHO’s Global Tricycle Surveillance and FAO’s AMR monitoring guidelines demonstrates Indonesia’s growing leadership in regional One Health implementation. Through open-access data, published findings, and policy briefs, the project offers a valuable contribution not only to the Indonesian AMR narrative but also to global health security.

Insights and Lessons Learned

The implementation of this genomic surveillance project revealed several compelling insights that may guide future One Health initiatives.

Firstly, the diversity of resistance patterns across regions underscored the importance of localized surveillance. Despite focusing on a single species—broiler chickens—and a consistent production context, the resistance gene profiles varied dramatically. Some regions exhibited dominance of blaCTX-M variants, while others had high levels of aminoglycoside or sulfonamide resistance genes. This finding debunks the myth of homogeneity in resistance trends and reinforces the necessity for region-specific interventions and tailored policy responses.

Secondly, it became abundantly clear that scientific data drives effective policy. The genomic findings were not confined to academic discussions—they were brought into high-level government panels, cited in national reporting documents, and considered in future strategic planning. Policymakers responded positively when presented with concrete evidence of regional AMR burdens. This underlines the critical role of data translation: research becomes impactful only when it is packaged in a way that supports decision-making.

Finally, the project illuminated the vital importance of capacity building in ensuring sustainability. From laboratory technicians to government veterinarians and student researchers, all actors benefited from training and mentorship embedded in the project. The use of complex tools like AMRFinderPlus, Linux bioinformatics pipelines, and Qubit DNA quantification was new to many participants. Yet with guided practice and collaborative learning, the team overcame technical barriers and became proficient. This growth in national technical capacity sets a strong foundation for Indonesia’s long-term AMR surveillance goals.

Conclusion

This project has not only expanded Indonesia’s AMR evidence base but has also transformed the way we engage with antimicrobial resistance. It demonstrated that genomic data can inform policy, drive education, and catalyze cross-sectoral collaboration. Supported by SEAOHUN and USDA, the initiative serves as a replicable model for integrated One Health programming across the region.

By investing in scientific rigor, local relevance, and institutional capacity, Indonesia is showing that genomic surveillance can be more than a research output—it can be a national health strategy.

Team Leader: Dr. med. vet. Hadri Latif, DVM, MSi, Division of Veterinary Public Health and Epidemiology, School of Veterinary Medicine and Biomedical Sciences, IPB University

Team Members:

• Imron Suandy, DVM, MVPH – Directorate General of Livestock and Animal Health, Ministry of Agriculture

• Dr. Puji Rahayu, DVM – Quality Control Laboratory and Certification of Livestock Products, Ministry of Agriculture

• Dr. Chaerul Basri, DVM, M.Epid. – IPB University

• Nofita Nurbiyanti, BVM – IPB University