Metagenomic Approach to Characterizing Disease Epidemiology in a Disease-Endemic Environment in Northern Thailand

Takhampunya, Ratree; Korkusol, Achareeya; Pongpichit, Chalermpol; Yodin, Komsan; Rungrojn, Artharee; Chanarat, Nitima; Promsathaporn, Sommai; Monkanna, Taweesak; Thaloengsok, Sasikanya; Tippayachai, Bousaraporn; Kumfao, Naruemon; Richards, Allen L.; Davidson, Silas A.

The discovery of certain bacterial pathogens was expected based on previous surveillance data and reported cases from the Ministry of Public Health. Additionally, other unexpected pathogens such as Anaplasma spp. and B. quintana (an agent causing Trench fever) were detected among UFI patients as well as Bor. miyamotoi in rodent populations. However, to date in-depth analyses as to how, when and where transmission occurs are lacking. Human, animal, and vector interactions play a major role in disease transmission and form a dynamic transmission cycle. Pathogens can spread from animal-toanimal or animal-to-human by several modes of transmission. Probably the most important method of transmission occurs during feeding by parasitic arthropods. This study employed NGS and metagenomics to characterize bacterial pathogens and understand their transmission in animal, human, and vector populations. Several pathogens were detected in rodent and vector populations indicating the complex ecology of bacterial pathogens and their reservoir hosts and vectors in the area close to where human activities occur which increase the risk of human-animal interface. The most apparent example is scrub typhus where O. tsutsugamushi was found in UFI patients, chiggers, and rodent populations. These data clearly illustrate the complex picture of pathogen transmission from animal reservoir hosts to humans via arthropod vectors. Local public health officials can effectively use the data to assist in understanding the seasonality of diseases such as scrub typhus and the populations most at risk. Information can be shared locally and preventive measures, such as repellents, can be used when appropriate. From this study, multiple bacterial pathogens known to cause human diseases in other locations were identified for the first time in Nan province. Such information is useful for local medical providers as they try to diagnose and treat patients with undifferentiated fevers. Finally, the data presented in this study effectively illustrate the utility of metagenomics in future epidemiological surveys involving multiple types of samples.