Optimization of DGGE community fingerprinting for characterizing Escherichia coli communities associated with fecal pollution

We evaluated the use of DGGE fingerprinting to differentiate communities of Escherichia coli from animal and geographic sources. An initial screening of 15 gene candidates revealed the ability of three target genes (mdh, phoE and uidA-4) to effectively differentiate E. coli communities originating in horses, pigs, geese and goats. Cluster and jackknife analyses performed on the communities from a more extensive number of hosts (n = 150) including humans (via raw sewage), horses, pigs, geese and cows revealed that the internal accuracy of classification of E. coli community fingerprints to their origin was similar for each of the three genes (85–86%). Each of the three genes were tested for their ability to associate E. coli source- and sink communities in two settings featuring contaminated water; (i) a stream receiving municipal wastewater effluent and (ii) a pond inhabited by geese. For each gene, DGGE fingerprints effectively matched effluent- and downstream E. coli communities (98–100% similarity) and excluded upstream communities, while communities from goose fecal material were 77–79% similar to communities in pond water, indicating fecal inputs from geese. Furthermore, each gene discriminated against E. coli communities from hosts non-indigenous to either setting. DGGE analysis of E. coli communities appears to be a promising tool to augment existing efforts aiming to address the dynamics of bacteria pollution in complex, natural environments.