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.

Several bacterial species were identified based on their highest similarity to reference sequences (GenBank database) as shown in Table 4 , as well as their identity (%) corresponding to highly matched reference sequences as indicated in parenthesis after each pathogen. Only some important pathogenic bacteria are discussed here. O. tsutsugamushi and Leptospira spp. are well-known pathogenic bacteria endemic to Thailand and were frequently detected in the samples studied. O. tsutsugamushi was detected among UFI patients, rodents, and chiggers and it was observed that some populations shared the same genotypes as demonstrated by the phylogenetic analysis present in Figure 5 . Although L. interrogans was confirmed to be present in rodent population, the pathogenic status of Leptospira spp. (NGS reads in the range 36-4,393) belonging to other populations could not be verified (Tables 3, 4) . B. quintana, the causative agent of trench fever, was detected in one UFI patient but not in other populations. However, other common rodent-associated Bartonella species were found in rodents and their associated fleas and lice. Interestingly, B. clarridgeiae, a possible causative agent of cat-scratch disease, was found in 2 pools of fleas (Ctenocephalides felis) collected from domesticated mammals FIGURE 5 | Phylogenetic tree analysis of O. tsutsugamushi genotypes detected among UFI patients, rodents, and chiggers in Nan province, Thailand (indicated in bold letters). A maximum likelihood tree was constructed based on 56-kDa type-specific antigen gene sequences using the GTR+G model of nucleotide substitution in the MEGA 6 program with bootstrapping (1000 replicates).