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.

Rodents and ectoparasites were collected during the wet (June-September) and dry (November-April) seasons in Bo Kluea, Mae Charim, and Phu Phiang districts of Nan province, Thailand in 2014-2018 (Figure 1 and Table 1 ). Ectoparasites were also collected from domesticated mammals (dogs, cats, and cattle). All study sites were on private land, and permission was obtained from each of the owners to conduct research on their land. None of the field studies involved endangered or protected species. Rodents were captured using live traps baited with bananas, palm fruit, or dried fish, and were collected from orchards, palm and rubber plantations, cultivated rice-fields, grassland areas, edges of dense forest, stream margins, and around dwellings. Traps were set for 3-5 nights and were checked early in the morning. Captured rodents were removed from the traps, euthanized using carbon dioxide, and processed immediately at the site of collection. Blood, serum, and tissue samples (liver, spleen, kidney, and lung) were collected and stored on dry ice. Ears were removed and stored in 70% ethanol for chigger collection. All tissues were then transported to the AFRIMS laboratory for further processing. All rodents were later identified to the species level as described previously (Muul, 1979) .