The Cross-Wellcome Africa Asian Programmes (AAPs) Acceleration of Genomics for Escalating Infectious Diseases (CAGED) Consortium is a collaboration among six institutions: the Africa Health Research Institute, the Center for Infectious Disease Research in Africa, the KEMRI-Wellcome Trust Research Programme, the Malawi Liverpool Wellcome Programme, the Mahidol Oxford Tropical Medicine Research Unit and the Oxford University Clinical Research Unit. The consortium focuses on studying drug-resistant pathogens driven by climate change and posing major public health threats in Africa and Southeast Asia including chikungunya (CHIKV), dengue (DENV), multidrug-resistant Klebsiella pneumoniae (Kpn), and drug-resistant Mycobacterium tuberculosis (Mtb). In this paper, we outline the consortium goals, planned activities, discuss challenges and future directions. By leveraging cross-continent expertise, CAGED aims to unravel the molecular epidemiology of escalating infectious diseases of public health importance in Africa and Southeast Asia, and build sustainable local sequencing capacity, helping the region better prepare for future emerging infectious disease outbreaks.