Abstract

Bacterial 16S ribosomal RNA (rRNA) genes contain nine “hyper-variable regions” (V1–V9) that demonstrate considerable sequence diversity among different bacteria. Species-specific sequences within a given hyper-variable region constitute useful targets for diagnostic assays and other scientific investigations. No single region can differentiate among all bacteria; therefore, systematic studies that compare the relative advantage of each region for specific diagnostic goals are needed. We characterized V6 and V1 to V6 regions of 16S-rRNA gene in 20 Pseudomonas, 15 Escherichia and 15 Klebsiella species including common urinary tract pathogens using different primer sets specifically designed to amplify different regions of our marker. We determined that the 167 nucleotides-long V6 region is not suitable for distinguishing all bacterial strains to the genus and species level and could not distinguish among all bacterial species especially Klebsiella strains. The 1073 nucleotides-long V1 to V6 region is more accurate than identification using sequence analysis of V6 region only and could identify all strains of unknown species Id. We also focused on how much sequencing information is needed for blind identification of bacterial pathogens. In conclusion, the DNA sequencing based method provides a valuable tool for cheap and accurate diagnosis of Gram-negative bacteria in urinary tract infections which can be applicable in other infections and in the diagnosis of other pathogenic bacteria.

Key words: Gram negative bacteria, urinary tract infections, 16S-rRNA gene, sequencing.