In Silico Study of Developing a Method for Detecting Pathogenic Bacteria in Refillable Drinking Water Samples

One of the parameters of quality of drinking water that is suitable for consumption is not contaminated by Escherichia coli , Salmonella and Shigella sp. Beside microbiological tests, water quality testing can be carried out molecularly only in few hours, using PCR (Polymerase Chain Reactions) technique. Although PCR is a basic molecular technique, various detection methods can be developed from it. The key to success in making a PCR-based method is inseparable from bioinformatics studies when designing primers that are specific to pathogen target DNA. The purpose of this research was to design pathogen-specific primers and do in silico study of PCR using bioinformatics software to get better planning in developing detection method. DNA sequence templates of E. coli , Salmonella and Shigella were downloaded from NCBI and multiple-aligned using Geneious Prime bioinformatic software. Primers were designed according to conserved region of these pathogens. The primers specificity was checked using Primer BLAST tools in NCBI. The result of this study was a pair of primers that amplify 825 bp fragment of 16S rRNA sequence specific to E. coli , Salmonella and Shigella .