**Abstract**

Neglected tropical diseases such as Chagas disease, dengue, Zika, chikungunya, and malaria cause millions of deaths each year and they are caused by a variety of pathogens whose diagnosis is very limited or subject to conventional testing, making a treatment less accessible, accurate and timely diagnosis for choosing their treatments. Traditional methods for pathogen detection have not been able to meet the growing need for diagnosis and control. The incorporation of new technologies such as nextgeneration sequencing (NGS) and digital PCR (dPCR) represent a better diagnostic possibility due to their ability to absolutely quantify pathogens with high selectivity and precision. Our planet is currently experiencing environmental changes of an unprecedented magnitude and rate, including climate change, globalized pollution, biodiversity loss, and land use changes, so neglected diseases require a comprehensive understanding of the ecology of vectors in the different eco-epidemiological contexts, as well as of the transmission cycles of pathogens and their transmission dynamics. In this sense, NGS and dPCR open a new panorama for a better understanding of these diseases with the aim of proposing new programs for their care.

**Keywords:** neglected tropical diseases (NTDs), DNA, metabarcoding, dPCR, next-generation sequencing (NGS), diagnosis, pathogen detection, digital droplet PCR (ddPCR), ecohealth
