DNA extraction using FTA Elute cards for detection and enumeration of fecal indicator bacteria in the Chao Phraya River, Thailand

Utilizing molecular methods for monitoring and determining water quality in developing countries can be problematic. Effective extraction and storage of DNA from environmental samples is especially difficult due to lack of access to sufficient laboratory facilities for molecular work. Use of a commercial product for the extraction of DNA, as well as its application in determining the microbial quality of surface waters, was evaluated and compared. Surface water samples collected from the Chao Phraya River in Thailand were processed to enumerate Escherichia coli. Quantification was done through culture methods (Colilert Quanti-tray) and quantitative real-time PCR (SYBR green and Taqman assays). Processing of surface water samples and culture enumeration of E. coli was done in Thailand, while DNA extraction and enumeration using real-time PCR was done in Korea. E. coli MPN counts were mean log 2.89/100ml. Quantitative real-time PCR assays counts ranged from 2.38 to 3.59 mean log CFU/100 ml. Taqman PCR assays had no significant difference in mean log counts compared to conventional culture methods. However mean log counts of SYBR green PCR assays were significantly higher than counts obtained by culture methods and Taqman PCR assays (P<0.05). Results demonstrated FTA Elute cards can be employed for the extraction of microbial DNA from surface waters and have potential use in detection of fecal indicator bacteria from environmental water sample