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.

In this study, metagenomics and NGS technology were used to characterize human (patients with undifferentiated febrile illness (UFI)), reservoir host (rodents and small mammals), and ectoparasite (chiggers, ticks, fleas, and lice) populations for bacterial pathogens. All samples were collected from Nan province in northern Thailand. Since all samples were from the same sites, bacteria could be compared from different populations to determine potential vectors and reservoirs. Nan province is highly endemic for scrub typhus, caused by the agent Orientia tsutsugamushi, and one of the major goals of this study was to determine the etiology and transmission dynamics of scrub typhus in the area. Another goal was to identify other bacterial pathogens that were under-reported or not previously known from this region. NGS results were verified by conventional methods such as real-time PCR, PCR, and DNA sequencing to confirm the pathogenic potential of detected bacteria and to better characterize those important pathogens to the species level. In addition, serological tests were performed to determine the seroprevalence and the history of human exposure to the pathogens detected by the NGS approach. The indepth characterization of bacteria performed in this study from humans, animal hosts, and ectoparasites allowed us to determine the transmission dynamics of pathogens and identify several new and previously unreported pathogens from this area.