The study underscores the importance of expanding genomics-based surveillance programs worldwide to identify pathogens and prevent future epidemics in resource-scarce, outbreak-prone settings.
Dengue, chikungunya, HIV, and leptospirosis were among the many pathogens detected in a recent Cambodia-based study that used cutting-edge genetic sequencing and geographic information science (GIS) to understand the causative agents behind febrile illnesses in Cambodia. The study, co-authored by assistant professor of population health and disease prevention at the UCI Program in Public Health Daniel M. Parker, PhD, reinforced the need for ongoing, coordinated genomics-based geographic surveillance worldwide to discover pathogens before they emerge at epidemic levels. This is especially important for parts of the world where resources are scarce and capacity for testing, lab diagnostics, and bioinformatics is limited.
The study was funded by the Bill & Melinda Gates Foundation and was just published online in the journal Proceedings of the National Academy of Sciences of the United States of America.
Parker and team used a spatial epidemiologic data system and a method of genomics-based surveillance called metagenomic next generation sequencing (mNGS) to identify pathogens responsible for fevers in a peri-urban area in Cambodia. In 2018 the team began a dengue surveillance project in peri-urban Cambodia, and they noticed that most of the children coming into the hospital with fever did not have dengue and never received a final diagnosis. The goal of this project was to attempt to find out what pathogens were causing all of these fevers.
The research team collected samples from over 480 patients aged 6 months to 65 years presenting with fever, then ran the samples through mNGS to determine which pathogens were present. Next, they mapped the home locations of the patients to look for associations between environmental and geographic factors and different pathogens.
“Dengue virus as the most abundant pathogen, partially because dengue cases almost globally exploded in 2019,” Parker said. “But we also detected several zoonotic and vector-borne pathogens like Plasmodium knowlesi (a type of malaria that comes from monkeys)andleptospirosis, and rickettsial diseases that are relatively common but challenging to diagnose or treat in resource-limited settings. That’s why it’s imperative that we implement genomics-based spatial surveillance programs on a wide scale to better monitor emerging diseases around the world. If we detect these pathogens early, we have a better chance at mounting a rapid, effective public health response.”
