The presence of Escherichia coli has long been established as the most reliable microbiological indication of fecal contamination in water. Current recommended culture-based methods for assessing water quality by the detection of E. coli are lengthy and lack ubiquity (ability to detect most if not all strains of a target microorganism). We describe rapid and sensitive conventional and real-time PCR assays specific to E. coli and Shigella, based on the nucleotide sequence of the highly conserved elongation factor Tu (tuf) gene enabling the detection of all members of the genospecies.