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.

After NGS analysis, eleven potential pathogenic bacteria were detected among samples. Table 2 shows details about positive NGS pools and the number of reads indicated by range for each potential pathogen detected among sample populations. Bartonella spp. were the most prevalent and detectable bacteria among samples studied and the highest infection rate was found in rodent population (47/64 NGS pools). Bartonella spp. were found in most sample types with the exception of ticks and lice from domesticated mammals (69/183 NGS pools). The second most prevalent bacteria was Anaplasma spp. (37/183 NGS pools) which was found in UFI patients (8/23), rodents (20/64) and rodent-associated ticks (5/17), and ticks collected from domesticated mammals (4/8). Rickettsia spp. were also found in high prevalence as well (30/183), mostly in pools of fleas collected from domesticated mammals (12/12), 10 out of 17 pools of rodent ticks, 4/8 pools of ticks from domesticated mammals, 3/64 pools of rodents, and 1/4 pools of rodent lice. Borrelia spp., FIGURE 3 | Taxonomic diversity and relative abundance at the phylum (A) and genus (B) level of bacterial community in UFI patients, rodents, chiggers, and ectoparasites collected from rodents, and ectoparasites collected from domesticated mammals. Phyla were identified on the basis of a confidence threshold cutoff of 77%, and genera on a confidence threshold cutoff of >90% using the Green Genes reference database. The percent relative abundances are of the total number of OTUs. Color legend for each phylum (A) or genus (B) was indicated below the bar graph.