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.

Wolbachia spp. was found mainly in mammal fleas (n = 10 NGS pools) with one pool each in rodents and ticks, lice, and fleas collected from rodents. The data of endosymbionts detected in NGS pools were provided as online Supplementary Data (Supplementary Figure S1) . Few reads were detected in UFI patients (273 reads). This may have been due to crosscontamination during the sample preparation process. Coxiella endosymbionts were equally found in ticks collected from rodents and domesticated mammals. Few (n = 2) were associated with Francisella spp., and they were suspected as endosymbionts since they tested negative by a confirmatory assay (qPCR and PCR). Only one NGS pool of chiggers was found to carry a Coxiella endosymbiont. Francisella endosymbiont was mainly found in chiggers and ticks collected from rodents but one pool was also found in ticks from a dog. Candidatus Cardinium was mostly detected in chiggers; however, it was also detected in one pool of rodent fleas and in one pool of rodent ticks. Rickettsia spp. were mainly detected in ticks and lice from rodents and fleas and ticks from domesticated mammals. However, some Rickettsia were pathogenic species as confirmed by real-time PCR and DNA sequencing. This phenomenon was mostly observed in Rickettsia from flea pools (mostly from domesticated mammals) where Rickettsia could be identified to species and excluded from being identified as endosymbiont bacteria. Therefore, Rickettsia endosymbiont was not discussed here. When considering only known and confirmed endosymbionts (Wolbachia, Coxiella, and Ca. Cardinium) found in vectors, there was usually one or two predominant endosymbionts harbored by each vector type.