During the last century, WHO have led public health interventions that resulted in spectacular achievements such as the worldwide eradication of smallpox and the elimination of malaria from the Western world. However, besides major successes achieved in control of infectious diseases, most elimination/control programs remain frustrating in many tropical countries where specific biological and socio-economical features have prevented implementation of disease control over broad spatial and temporal scales. Emblematic examples include malaria, dengue, yellow fever, measles and HIV. There is consequently an urgent need to develop affordable and sustainable disease control strategies that can target the core of infectious disease transmission in highly endemic areas. Although on the one hand most pathogens are resistant to elimination, on the other hand, paradoxically, human activities are major drivers of the current high rate of extinction among higher organisms through alteration of their ecology and evolution, i.e., their "niche". During the last decades, the accumulation of ecological and evolutionary studies focused on infectious diseases has shown that the niche of a pathogen holds more dimensions than just the immune system targeted by vaccination and treatment. Indeed, it comprises various intra- and inter- host levels at very different spatial and temporal scales. This project aims to shift from disease control to reverse conservation biology of pathogens in order to devise new public health strategies. Our objective is a qualitative understanding of the “niche” of two different pathogens at a fine spatial scale, Plasmodium falciparum in Bobo-Dioulasso (Burkina-Faso) and Dengue virus in Kâmpóng Cham (Cambodia), through a trans-disciplinary approach mixing ecology of infectious diseases, public health and health economics to carefully tailor mathematical models able to demonstrate how public health strategies could be improved for these diseases control in these areas and potentially drive the pathogens to local extinction. Such public health tools could be thus extended to other areas of interest and other diseases.