Aims: To investigate human viral contamination in urban rivers and its impact on coastal waters of southern California, USA. Methods and Results: Three types of human viruses (adeno, entero and hepatitis A) were detected using nested- and RT-PCR from 11 rivers and creeks. Faecal indicator bacteria as well as somatic and F-specific coliphage were also tested. Approximately 50% of the sites were positive for human adenoviruses. However, there was no clear relationship between detection of human viruses and the concentration of indicator bacteria and coliphage. Both faecal indicator bacteria and human viral input at beaches near river mouths were associated with storm events. The first storm of the wet season seemed to have the greatest impact on the quality of coastal water than following storm events. Conclusions: This study provides the first direct evidence that human viruses are prevalent in southern California urban rivers. Urban run-off impacts coastal water quality most significantly during the storm season. Significance and Impact of the Study: To protect human health during water recreational activities, it is necessary to develop effective strategies to manage urban run-off during storm events.

Real-time PCR was applied to quantify the abundance of human adenoviruses in two southern California urban rivers, the San Gabriel and Los Angeles. A total of 114 river samples from five different locations were collected over a 1-year period and analyzed for human adenoviruses, along with fecal indicator bacteria and coliphages. Adenoviruses were detected by real-time PCR in similar to 16% of the samples, with concentrations ranging from 10(2) to 10(4) genomes per liter. However, a plaque assay using two human tissue culture cell lines, HEK-293A and A549, yielded negative results, suggesting that adenoviruses detected by real-time PCR are likely noninfectious. Enterovirus genome was detected in similar to 7% of the samples by reverse transcription-PCR. Analysis by Spearman's rho rank order correlation showed significant correlations between fecal indicator bacteria and indicator virus (total coliform, fecal coliform, enterococcus, and coliphage values). However, no significant correlations were found between human adenoviruses quantified by real-time PCR and culturable coliphages or fecal indicator bacteria. Kruskall-Wallis chi-square analysis showed significant seasonal variability of all fecal indicator bacteria and coliphages, while no significant variability was observed for adenoviruses or enteroviruses. This study presents the first quantitative measurement of human adenovirus genomes in urban rivers and their statistical relationship to fecal indicator bacteria and coliphages. The uncoupling between high-number genome copies of adenoviruses detected by real-time PCR and the absence of infectivity detected by tissue culture suggests that genome-based detection methods are inadequate for direct assessment of human health risk.

Microbial pathogens in the environment present a growing threat to human health. They are found in waters used for recreation, irrigation etc., which present a multitude of pathways in which a person may be exposed to them. Moreover, the increasing interest in reusing treated wastewater raises questions of water quality and associated public health risks. The overarching goal of my dissertation is to develop quantitative tools to improve the accuracy of methods used to assess this risk and provide insights into disease development. I hypothesize that mathematical models rooted in well-grounded theory and data can augment the overall understanding of microbial risk and steer experiments in the most productive direction. My specific aims are: 1) To quantify the health risk posed by norovirus-contaminated water used for lettuce irrigation, by means of a dynamic transport model 2) To develop a dose-response framework applicable for antibiotic resistant bacteria, specifically the human enteric pathogen, Escherichia coli 3) To develop a modeling framework to probe the importance of cooperativity in helping Staphylococcus aureus establish skin infections. In my research, I have constructed a transport model using ordinary differential equations to predict the norovirus load in lettuce at harvest given the load in the irrigation water. By fitting this model to published experimental data, I found that attachment of the virus to the growth medium strongly influences the amount of virus in lettuce at harvest. Towards the second aim, I have used stochastic processes to develop an analytical expression for E. coli dose-response. I then fitted this to clinical data and extended the model to predict, for the first time, the risk posed by a mixture of antibiotic sensitive and antibiotic resistant strains. Towards the third aim, I have developed a two-compartment stochastic model with cooperativity between cells to predict S. aureus dose-response. Using experimental data to reject the hypothesis of absence of cooperativity, I show the possible role of quorum sensing in S. aureus establishing skin infections. The outcomes of this research will enable better understanding of microbial risk associated with environmental exposure and improve human health protection.

Pathogenic bacteria and enteric viruses can be introduced into the environment via human waste discharge. Methods for rapid detection and quantification of human viruses and fecal indicator bacteria in water are urgently needed to prevent human exposure to pathogens through drinking and recreational waters. Here we describe the development of two real-time PCR methods to detect and quantify human adenoviruses and enterococci in environmental waters. For real-time quantification of enterococci, a set of primers and a probe targeting the 23S rRNA gene were used. The standard curve generated using Enterococcus faecalis genomic DNA was linear over a 7-log-dilution series. Serial dilutions of E. faecalis suspensions resulted in a lower limit of detection (LLD) of 5 CFU/reaction. To develop real-time PCR for adenoviruses, degenerate primers and a Taqman probe targeting a 163-bp region of the adenovirus hexon gene were designed to specifically amplify 14 different serotypes of human adenoviruses, including enteric adenovirus serotype 40 and 41. The standard curve generated was linear over a 5-log-dilution series, and the LLD was 100 PFU/reaction using serial dilutions of purified adenoviral particles of serotype 40. Both methods were optimized to be applicable to environmental samples. The real-time PCR methods showed a greater sensitivity in detection of adenoviruses in sewage samples than the viral plaque assay and in detection of enterococci in coastal waters than the bacterial culture method. However, enterococcus real-time PCR overestimated the number of bacteria in chlorinated sewage in comparison with the bacterial culture method. Overall, the ability via real-time PCR to detect enterococci and adenoviruses rapidly and quantitatively in the various environmental samples represents a considerable advancement and a great potential for environmental applications.

We constructed a simulation model to compute the incidences of highly credible gastrointestinal illness (HCGI) in recreational bathers at two intermittently contaminated beaches of Orange County, California. Assumptions regarding spatial and temporal bathing patterns were used to determine exposure levels over a 31-month study period. Illness rates were calculated by applying previously reported relationships between enterococcus density and HCGI risk to the exposure data. Peak enterococcus concentrations occurred in late winter and early spring, but model results showed that most HCGI cases occurred during summer, attributable to elevated number of exposures. Approximately 99% of the 95,010 illness cases occurred when beaches were open. Model runs were insensitive to 0-10% swimming activity assumed during beach closure days. Comparable illness rates resulted under clustered and uniform bather distribution scenarios. HCGI attack rates were within federal guidelines of tolerable risk when averaged over the study period. However, tolerable risk thresholds were exceeded for 27 total days and periods of at least 6 consecutive days. Illness estimates were sensitive to the functional form and magnitude of the enterococcus density-HCGI relationships. The results of this study contribute to an understanding of recreational health risk in coastal waters.