Pathogen genomics to inform control of antimicrobial resistant pathogens: an assessment of readiness and potential impact in the ASEAN region

Technical Summary: Pathogen Genomics to Inform Control of Antimicrobial Resistant Pathogens in the ASEAN Region

Problem Statement
Antimicrobial resistance (AMR) represents a critical global and regional health threat, with the Southeast Asian region bearing the highest burden of AMR, where one in three laboratory-confirmed infections involves antibiotic-resistant bacteria. While all ten ASEAN nations have established National AMR Action Plans aligned with the World Health Organization (WHO) Global Action Plan, significant gaps persist in national surveillance systems and the effective utilization of data for action at sentinel, national, and regional levels. Current surveillance often lacks the high-resolution insights necessary to identify transmission pathways, emerging resistance mechanisms, and outbreaks. Although pathogen whole-genome sequencing (genomics) offers these capabilities, its integration into routine AMR control in the ASEAN region remains uneven. There is a need to assess the readiness of national reference laboratories and sentinel sites in the Philippines, Malaysia, and Thailand to implement genomics-enabled surveillance and to evaluate the potential impact of such integration.

Methodology
This study employed a collaborative, regionally coordinated initiative involving the Research Institute for Tropical Medicine (Philippines), the National Institute of Health (Thailand), the Institute for Medical Research (Malaysia), and the Centre for Pathogen Genomics at the University of Melbourne (Australia). The assessment was conducted in 2026 through a multi-faceted approach:

1. Scoping Surveys: Sentinel sites completed surveys detailing current practices in AMR data generation, specimen selection, data management, reporting, and workforce training.
2. Workshops: Participatory workshops were held in each country involving microbiologists, clinicians, infection control nurses, and data managers. These sessions utilized data and isolate flow mapping exercises to visualize current workflows, identify stakeholders, and pinpoint barriers.
3. Site Visits and Consultations: Technical partners conducted visits to national reference laboratories and sentinel sites to complement workshop findings.
4. Readiness Framework: Readiness was assessed across four thematic domains aligned with the WHO International Pathogen Surveillance Network:
   • Governance: Strategic planning, funding, and coordination.
   • Assets and Workforce: Sequencing platforms, bioinformatics infrastructure, and staffing.
   • Processes and Continuous Improvement: Standard operating procedures (SOPs), quality assurance, and sample availability.
   • Data Analysis and Decision Making: Data governance, interoperability, reporting timeliness, and integration into decision-making.

Data were synthesized qualitatively to categorize readiness levels as "foundational," "implemented," or "embedded," with cross-country comparisons to identify common gaps and specific needs.

Key Contributions and Results
The study identified that while the Philippines, Malaysia, and Thailand possess a strong foundation for AMR surveillance, significant barriers hinder the transition to routine, genomics-enabled surveillance.

• Current Status: All three countries have established National AMR Action Plans and reference laboratories equipped with Illumina and Oxford Nanopore sequencing platforms. Trained staff exist at national levels, and sentinel sites have developed capacity in microbiology and infection control.
• Identified Barriers:
  • Governance and Funding: Funding for genomics is largely project-based or unpredictable, lacking multi-year commitments or routine budget allocation.
  • Data Interoperability: There is a lack of interoperability between hospital and laboratory information systems, leading to delays in data integration and reporting.
  • Turnaround Time: Current reporting timelines from reference laboratories are too long to inform real-time clinical management or outbreak response at sentinel sites.
  • Workforce Gaps: While national sites have capacity, there is a need for increased genomic literacy and training at the sentinel site level to ensure data can be acted upon.
  • Standardization: SOPs for bioinformatics and data analysis require standardization, and quality control for genomic sequencing varies, particularly in Malaysia.
• Data Flow Findings: Mapping exercises revealed that while phenotypic data is used for local antibiograms and national reporting, genomic data is not yet integrated into real-time decision-making. Existing referral pathways exist but are often batched due to resource constraints.

Potential Impact and Opportunities
Participants identified that integrating genomics could provide high-resolution data on resistance mechanisms, isolate relatedness, and outbreak detection currently unavailable at the hospital level. The study outlines three key strategic opportunities:

1. Routine Surveillance: Implementing genomics to characterize transmission of critically resistant pathogens and developing platforms for automated, real-time reporting.
2. Evidence Generation: Conducting pilot projects to generate context-specific evidence on the health and economic burden of resistant pathogens to support sustainable funding.
3. Regional Prioritization: Integrating genomic and phenotypic data across borders to understand regional resistance patterns and strengthen coordination against emerging threats.

Impacts were categorized into short-term (outbreak management, antimicrobial stewardship), medium-term (improved stakeholder communication), and long-term (policy development and budget allocation).

Significance and Claims
The paper asserts that the Philippines, Malaysia, and Thailand are well-positioned to progressively implement nationally led and regionally coordinated genomics-enabled AMR surveillance. The study highlights that while retrospective genomic sequencing has already uncovered outbreaks and plasmid transmission in these countries, the standardised, routine implementation of timely genomics is required to unlock its full potential for patient care and policy development.

The authors claim that this assessment provides a roadmap for moving from retrospective research to proactive, real-time surveillance. They emphasize that success requires coordinated, phased implementation focusing on:

• Developing robust governance and data-sharing frameworks.
• Establishing secure platforms for data storage, analysis, and visualization.
• Ensuring timely reporting to meet end-user needs.
• Evaluating impact to inform expansion and sustained funding.

The study concludes that while readiness is uneven, these nations can harness leadership from national reference laboratories to advance genomic surveillance, ultimately supporting data-driven policy and improved patient outcomes across the ASEAN region. The authors note limitations, including the small number of sentinel sites assessed and the focus on human health, acknowledging that further work is needed to assess One Health sectors and formally evaluate the economic impact of these interventions.