Pathogens are constantly evolving, driving the emergence of more transmissible variants and accelerating antimicrobial resistance (AMR), one of the most pressing threats to global health today. As infectious diseases continue to cross borders with increasing speed, effective public health responses require more than conventional surveillance, they demand real-time genomic intelligence that can detect, monitor, and anticipate pathogen evolution.

To address this challenge, the Collaborative African Genomics and Disease Epidemiology for Monitoring and Analysis of Disease through Zoonotic and Infectious Pathogens (CAGED-MADZIP) initiative brings together partners across the Asia-Pacific and Africa to strengthen genomic surveillance and translate genomic insights into actionable public health interventions. In Indonesia, the program is implemented by Summit Institute for Development (SUMMIT) across two strategic sites—Lombok and Purbalingga—where genomic data is integrated with epidemiological evidence to support faster, more informed public health decision-making.

At SUMMIT, genomic surveillance is not viewed as an isolated laboratory activity. It is part of a broader ecosystem that connects molecular science, epidemiology, health systems, and frontline healthcare. The ultimate objective is to transform scientific evidence into practical solutions that improve population health outcomes.

The CAGED-MADZIP program focuses on three priority pathogens that represent major public health challenges in Indonesia and globally: Dengue virus (DENV), Mycobacterium tuberculosis (MTB), and Klebsiella pneumoniae (KPN). Each pathogen presents distinct epidemiological challenges, yet all share a common need for timely detection, comprehensive surveillance, and evidence-based intervention.

Dengue remains one of the world's most significant vector-borne diseases, with transmission occurring in more than 100 countries, including Indonesia. In 2024, global dengue cases surged dramatically, affecting an estimated 14 million people. Indonesia alone reported more than 210,000 cases and approximately 1,200 deaths by November 2024. This unprecedented increase reflects the complex interaction of environmental change, vector dynamics, human mobility, and viral evolution.

Through genomic surveillance, SUMMIT characterizes circulating dengue serotypes and genotypes, reconstructs transmission dynamics, detects emerging variants, and identifies genetic changes that may influence virulence, transmissibility, and vaccine effectiveness. These insights strengthen outbreak preparedness and provide critical evidence for designing more effective dengue control strategies.

Tuberculosis continues to be one of the deadliest infectious diseases worldwide, affecting approximately 10 million people and causing around one million deaths every year. The emergence of multidrug-resistant tuberculosis further complicates disease control, highlighting the need for more precise surveillance tools.

By applying whole genome sequencing, SUMMIT enables high-resolution mapping of transmission networks, early identification of drug resistance-associated mutations, and comprehensive characterization of strain diversity. These genomic insights support targeted treatment decisions, improve contact investigation, and strengthen national tuberculosis control efforts through more precise epidemiological understanding.

Another growing concern is Klebsiella pneumoniae, an opportunistic bacterial pathogen responsible for severe healthcare-associated infections and rapidly increasing antimicrobial resistance. The organism accounts for approximately ten percent of hospital-acquired infections and poses a particularly serious threat in intensive care units, neonatal wards, and maternal health services.

Within the CAGED-MADZIP framework, genomic surveillance of Klebsiella pneumoniae focuses on identifying antimicrobial resistance determinants, tracing transmission pathways within healthcare facilities, and detecting outbreak clusters before they expand. These findings provide essential evidence for strengthening infection prevention and control measures, particularly in neonatal sepsis, maternal sepsis, and post-cesarean surgical site infections.

Central to this work is SUMMIT's implementation of Whole Genome Sequencing (WGS) using Oxford Nanopore Technologies platforms. Unlike conventional molecular diagnostics that target only selected regions of a pathogen's genome, WGS captures complete genomic information, enabling comprehensive characterization of genetic variation, antimicrobial resistance mechanisms, evolutionary patterns, and transmission pathways.

Oxford Nanopore sequencing technology offers rapid, portable, and scalable genomic analysis, making it particularly well suited for resource-limited and field-based settings. Its ability to generate near real-time genomic data enables faster outbreak detection, supports timely public health interventions, and enhances evidence-based decision-making across diverse healthcare environments.

However, what distinguishes SUMMIT is not only the technology it employs, but the philosophy that guides its research.

At SUMMIT, scientific discovery is meaningful only when it creates tangible benefits for communities. Research is intentionally designed to bridge laboratory science with real-world public health practice, ensuring that every genomic insight contributes to stronger health systems and better health outcomes.

This multidisciplinary approach integrates laboratory science, epidemiology, and public health into a unified research ecosystem. For example, sequencing efforts for neonatal and maternal sepsis extend beyond molecular characterization; they are linked to epidemiological profiles, healthcare delivery systems, and frontline clinical practice to generate a comprehensive understanding of disease transmission and patient outcomes.

Equally important is the continuous feedback loop between research and implementation. Rather than remaining within academic publications, research findings are translated into actionable recommendations for healthcare providers, policymakers, and local communities. This process strengthens primary healthcare services, informs disease control strategies, and supports evidence-based health policy at both local and national levels.

By combining cutting-edge genomic technologies with multidisciplinary collaboration and community-centered implementation, SUMMIT is building a sustainable model for genomic surveillance that extends far beyond pathogen sequencing. The CAGED-MADZIP initiative demonstrates how genomic science can become a practical public health tool, one that enables earlier detection of outbreaks, more effective control of antimicrobial resistance, and stronger preparedness for future infectious disease threats.

Ultimately, SUMMIT's mission goes beyond generating scientific knowledge. It is committed to pioneering research that is rigorous, collaborative, and impactful, transforming evidence into sustainable health solutions that improve lives across Indonesia and contribute to global health security.