Identification of microbial pathogens from deep sequencing in humans and rats from the Mekong Delta, Vietnam.

Abstract

The emergence of enzootic zoonoses have seen worrying growth recently. This is in part through the advent of better means of travel and increased population growth, setting off a perpetual arms race of coevolution pitting host and parasite against one another resulting in the loss of billions in dollars annually and thousands of lives. In recent years, South Asia has been identified as a hotspot for emerging infectious disease due to its rapid population growth and closeness to disease causing species. In an effort to stem the rapid rise of pathogen infection and emergence of infectious diseases, we utilized samples collected from a known rodent vector, Rattus argentiventer, and rat traders from open air meat markets in the Mekong Delta to identify potential viruses, monitor microbial diversity, and identify any potential spill over from rats to humans. These samples were taken from 300 individuals. Of these total samples, 250 humans were split between a control set and rat traders; with the remaining 50 being rat samples. These samples were comprised of respiratory swabs and blood plasma samples. We identified bacteria from samples using next-generation sequencing and bioinformatic tools and performed diversity analyses utilizing the OneCodex database as the comparison library. It was established that there were a number of rodent borne pathogens within the human population of the tested locations, in both human controls as well as the rat traders themselves. It was ultimately concluded that based on the results, a definitive answer cannot be made on potential spill over due to the infection of human controls with rodent borne viruses. However, it can be affirmatively concluded that there are a number of disease causing bacteria, rodent in origin, within the larger population of all humans in tested regions in the Mekong Delta.