The lack of appropriate methodology for tracing bacterial contamination sources greatly impedes the identification and control of these environmental pollutants. This in turn, adversely affects the decision-making process in water quality management. Several methods have been utilized for tracking genetically engineered microorganisms including ribotyping, PFGE, antibiotic resistance analysis, rep-PCR and carbon source utilization.

However, the utility of these methods are limited to the detection of organisms carrying reporter genes or their products. Efforts to track sources of natural bacterial populations have been made with partial success as the approaches used were based upon quantification of indicator organisms at various sites. Nonetheless, these studies invariably have raised more questions than answers.