Pathogens are constantly evolving, driving the emergence of more transmissible variants and accelerating antimicrobial resistance, which poses an urgent and ongoing threat to global health. CAGED-MADZIP is a collaborative initiative across the Asia-Pacific and Africa aimed at strengthening genomic surveillance and translating genomic insights into actionable public health interventions. In Indonesia, the project is implemented across two sites: Lombok and Purbalingga.

The program focuses on key pathogens responsible for major infectious diseases, including Dengue viruses, Mycobacterium tuberculosis, and Klebsiella pneumoniae. By integrating genomic and epidemiological data, CAGED-MADZIP strengthens outbreak detection, tracks pathogen evolution, and supports timely, evidence-based public health responses.

Dengue Virus (DENV)

Dengue is a major vector-borne disease endemic in more than 100 countries, including Indonesia. In 2024, global cases surged dramatically, affecting an estimated 14 million people. In Indonesia alone, over 210,000 cases and approximately 1,200 deaths were reported by November 2024. This increase is driven by a combination of environmental factors, human behavior, vector dynamics, and viral evolution.

Genomic surveillance of DENV aims to characterize circulating serotypes and genotypes, resolve transmission dynamics, detect emerging variants, and identify genomic changes that may impact virulence, transmissibility, and vaccine effectiveness.

Mycobacterium tuberculosis (MTB)

Tuberculosis remains one of the leading infectious diseases worldwide, affecting around 10 million people annually and causing approximately 1 million deaths. As a respiratory disease caused by Mycobacterium tuberculosis, its continued burden is exacerbated by delayed detection and the rise of drug-resistant strains.

Genomic surveillance of MTB enables high-resolution mapping of transmission networks, early detection of resistance-associated mutations, and characterization of strain diversity, thereby informing targeted treatment strategies and strengthening tuberculosis control efforts.

Klebsiella pneumoniae (KPN)

Klebsiella pneumoniae is a critical and rapidly evolving pathogen associated with severe infections and escalating antimicrobial resistance. It is a major contributor to morbidity and mortality, particularly among vulnerable populations, and accounts for approximately 10% of nosocomial infections, with higher prevalence in intensive care settings.

Genomic surveillance of KPN focuses on the identification of antimicrobial resistance determinants, characterization of transmission pathways within healthcare settings, and detection of outbreak clusters. These efforts are essential for guiding infection prevention and control strategies, particularly in the context of neonatal sepsis, maternal sepsis, and post–cesarean surgical site infections.

Summit Institute for Development employs a cutting-edge approach by implementing whole genome sequencing (WGS) to generate high-resolution, comprehensive insights into pathogen dynamics. By sequencing entire genomes, this approach enables detailed characterization of genetic variation, identification of antimicrobial resistance determinants, and reconstruction of transmission pathways across populations and settings. The laboratory utilizes Oxford Nanopore Technologies platforms, which provide rapid, portable, and scalable sequencing capabilities. This allows for near real-time data generation, supporting timely outbreak detection and evidence-based public health responses, particularly in resource-limited and field-based settings.