The use of molecular and genomic tools to examine the population structure of Escherichia coli in the environment

Fecal contamination of water is a widespread public health problem throughout the world. In developing countries, contamination of water by fecal material is a persistent threat to public health, where water-borne diarrheal disease is responsible for a significant number of deaths. The magnitude of contamination is determined by the enumeration of fecal indicator bacteria, including Escherichia coli. While E. coli is often thought of as a harmless commensal organism in the lower intestine of warm-blooded animals, pathogenic strains capable of causing severe disease and naturalized with the ability to grow in the environment also exist. In this dissertation, I describe several studies concerning E. coli in the environment which have implications for future water quality studies and are of interest to other researchers in the field, in addition to water quality regulators, beach managers, and public health professionals.;In the first study, I describe the isolation of DNA markers specific to E. coli originating from waterfowl for use in a culture-based, library independent method for microbial source tracking. This system used a DNA subtraction procedure to enrich for waterfowl-specific sequences which were then tested for specificity in colony hybridization assays. These markers were capable of identifying greater than 70% of waterfowl E. coli , while cross hybridization with strains from other hosts averaged about 10%.;An additional study focused on the use of the waterfowl E. coli DNA marker system and a high throughput, semi-automated robotic system to develop a macroarray colony hybridization assay for large scale quantitative detection of E. coli originating from waterfowl. This methodology was used to study the fecal input from waterfowl in two Minnesota lakes.;The high throughput system robotic system used in the source tracking study was adapted to screen large numbers of E. coli isolates obtained from a contaminated beach in California for the presence of virulence genes. The results of this study indicated that potential enteropathogenic E. coli (EPEC) strains were consistently detected in the water, which may represent a public health risk to recreational beach users.;Finally, I describe a study examining the spatial and temporal changes in E. coli populations present in the water and sediments in a small stream in south central Minnesota using a variety of molecular methods. This study indicated persistent E. coli strains are likely impacting the creek and that flow conditions and other environmental factors are likely dominant processes affecting E. coli populations in the creek.