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.

Conventional diagnostic tests used by most reference laboratories require culture, microscopy, serology, and polymerase chain reaction (PCR). Such tools are useful for pathogen detection but only if culture conditions, test sensitivity, and primers are compatible and suitable for the microbial target. Other molecular approaches can be used to capture a wider range of pathogenic species such as multiplex PCR that targets highly conserved DNA regions or multiplex assays that target many of the most common pathogens known to cause similar symptoms. However, it is worth noting that even when multiplex assays are used, pathogens not included in the multiplexing may go undetected. The use of 16S rDNA was first proposed by Woese and Fox (1977) and Woese et al. (1990) as a tool for the molecular identification and characterization of microorganisms. The 16S rDNA gene is highly conserved among prokaryotes and some parts of its sequence are hypervariable between species, which makes it an ideal marker for species identification and for understanding evolutionary relationships (Gill et al., 2006; Sogin et al., 2006; Dethlefsen et al., 2008; McInerney et al., 2008; Tringe and Hugenholtz, 2008; Sunagawa et al., 2009) . Metagenomics allows for comparisons of genetic material from multiple samples. One of the most common metagenomic approaches is deep amplicon sequencing (DAS), which employs universal primer to amplify parts of the 16S rRNA gene from specimens. A major benefit of metagenomics is the simultaneous detection of all microorganisms in clinical samples without prior knowledge of their identities. In addition, metagenomics has the potential to detect rare and novel pathogens. Current surveillance assays are limited in their ability to detect the emergence of novel pathogens or ones not previously known to be present in a given region. Metagenomic approaches can fulfill such gaps by identifying unknown etiological agents and assisting in the development of a new test for pathogen detection (Miller et al., 2013; Mokili et al., 2013; Wan et al., 2013) .