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

Background The ASEAN region has high rates of drug-resistant bacterial diseases. While pathogen whole genome sequencing (pathogen genomics) provides high resolution, actionable insights for control of antimicrobial-resistant pathogens, integration of pathogen genomics for antimicrobial resistance (AMR) control is limited in Southeast Asia health systems. We aimed to assess readiness for genomics-enabled AMR surveillance and response across three countries (the Philippines, Thailand, Malaysia). Methods Structured workshops were conducted with participants from sentinel sites, national reference laboratories and research institutes in 2026. A readiness assessment framework was applied to each country, complemented by a data and isolate flow mapping exercise. Data were synthesised and compared cross-country to identify common gaps and country-specific needs. Results All countries have strong foundations, with processes for isolate referral and critical AMR alerts at sentinel sites, and sequencing platforms at national reference laboratories. Common barriers included limited system interoperability and data integration, long turnaround times, and limited governance frameworks. Potential impacts of genomics-enabled AMR surveillance include faster detection of outbreaks, timely interventions, and a better understanding of national trends and inter-hospital transmission. Discussion These countries are well placed to implement a coordinated approach to AMR genomics, anchored in leadership from national reference laboratories, while ensuring data value is achieved both at national, regional and sentinel site levels. Advances in genomic surveillance for AMR will be facilitated by robust governance, data harmonisation and integration, and demonstrated utility for public health and clinical end-user.