Presents a state-of-the-art review of the current technology and applications being utilized to identify sources of fecal contamination in waterways. - Serves as a useful reference for researchers in the food industry, especially scientists investigating etiological agents responsible for food contamination. - Provides background information on MST methods and the assumptions and limitations associated with their use. - Covers a broad range of topics related to MST, including environmental monitoring, public health and national security, population biology, and microbial ecology. - Offers valuable insights into future research directions and technology developments.

ABSTRACT: Waterborne pathogen presence caused by fecal pollution is a leading cause of morbidity and mortality worldwide. In developed countries, this problem can result in waterborne outbreaks. Research suggests that there is a need for better fecal indicators because current methods (total coliforms and E. coli) are insufficient. This study investigated Bacteroidales 16S rRNA markers as a microbial source tracking tool in an agricultural watershed. Correlations between pathogens and markers were also investigated. Water quality monitoring was conducted following assay validation of ruminant-, bovine-, human-specific, and universal Bacteroidales markers. Results revealed a positive relationship between E. coli and the universal marker. Ruminant- and bovine-specific marker detection was associated with increased runoff due to precipitation; however, the human associated marker was not detected. Furthermore, no correlations between Campylobacter, Salmonella, or E. coli O157:H7 could be made. Consequently, these techniques have potential to become a powerful tool; however, further research is needed

University of Washington Abstract Enteric Virus Surveillance and Microbial Source Tracking in Fresh and Marine Waters of the Seattle Area Elena Jaffer Chair of the Supervisory Committee: Dr. John Scott Meschke Department of Environmental and Occupational Health Sciences Introduction: (Part I.) Bacterial indicators, including fecal coliforms, E. coli, and Enterococci, serve as long-standing measures of fecal contamination. However, coliphages hold promise as viral indicators, which may be more representative of viral enteric pathogens. Filtration and concentration of large water sample volumes (i.e. 20 L) increases viral detection sensitivity. (Part II.) Poverty Bay spans 11 shoreline miles of Puget Sound west of Des Moines. In response to recent geoduck bed closures in the area, we performed a microbial source delineation study in 5 creeks upland from the Bay with the intent of discovering the source of fecal contamination. Methods: (I.) Using the Bag-Mediated Filtration System (BMFS), followed by PEG precipitation and Vertrel XF extraction, we quantified levels of enteric viruses (AdV, NoV, EnV) and male-specific coliphage (MSC) at Green Lake, Lake Washington, and Puget Sound recreational beaches during June-November 2016. MSC was enumerated using the double agar layer, and enteric viruses were detected with qPCR. These data were compared to MPN estimates for traditional fecal indicator bacteria, using Colilert®-18 and Enterolert® substrates sealed in QuantiTrays®/2000. (II.) Coliscan Easygel ® kits were used during September 2016 – May 2017 to estimate E. coli levels in 5 streams upland of Poverty Bay during wet and dry weather conditions. Results: (I.) Throughout the sampling period (n = 6-7 samples/site), detection of MSC occurred only following a wet weather event, at levels of 19 PFU/L (Matthews Beach) and 21 PFU/L (Carkeek Beach). No pathogenic enteric viruses were detected with qPCR throughout the sampling period. However, a number of indicator bacteria samples exceeded U.S. EPA and Washington State standards during the sampling period. (II.) E. coli levels across the Poverty Bay drainage basin led to identification of potential hotspots on the 5 upland creeks. Significance: Unique to the Seattle Area, this study provides an overview of bacterial indicator, coliphage, and enteric virus levels in both fresh and marine waters. In addition, it contributes to the body of literature that evaluates the potential of coliphages to more accurately indicate fecal contamination than traditional bacterial indicators.

Fecal pollution of surface water is a significant environmental health issue. Indicator organisms are used to monitor microbial water quality, but often their presence does not coincide with the presence of pathogens. Bacterial source tracking is a term describing methods to determine the origin of fecal pollution based on bacterial traits. The objective of this research is to evaluate the use of 2 bacterial source tracking techniques, antibiotic resistance analysis (ARA) and ribotyping, to determine the sources of bacteria isolated from Sinking Creek. Based on the results of this study, ARA and ribotyping are not useful techniques for identifying sources of fecal pollution in Sinking Creek. ARA classification rates were low, and ribotype pattern generation success was 37%. The results of this study bring into question the reliability and reproducibility of these 2 source tracking methods for routine use in small watersheds.

Advisors: Prof. Charles N. Haas. L.D. Betz.

The molecular based, quantitative PCR assay was compared with the traditional viable E. coli count assay and a significant (P