Understanding fecal contamination dynamics through the integration of molecular pathogen quantification and land-water interface characteristics

To reduce public health risks and related economic losses, federal guidelines have been established to ensure surface waters meet water quality standards. For example, the United States Environmental Protection Agency released criteria in 1986 that recommended state and local governments establish and enforce regulations to protect ambient waters against naturally-occurring or anthropogenic contaminants. Most of the regulations that were enacted were designed to address recreational water quality because of the risk of illness associated with contact and ingestion of contaminated recreational waters. It wasn’t until 26 years after US EPA’s 1986 release of criteria that new guidance was issued regarding updated tools for managing recreational surface waters. In this report, US EPA included updated recommended criteria for acceptable levels of fecal indicator bacteria, E. coli and enterococci, within surface waters, while also introducing recommended molecular tools. In this dissertation, I applied these molecular methods with current regulatory tools, in an eastern North Carolina (NC) estuary heavily influenced by tidal inundation to better understand potential environmental drivers of surface water contaminant transport. Additionally, enterococci, which is the FIB used for NC’s regulatory assessment of surface water quality, can also be forecast using predictive modeling tools such as multiple linear regression (MLR) models. Similar to what was recommended with regards to incorporating molecular approaches, predictive modeling tools were also a newly suggested monitoring tool recommended by US EPA in the 2012 update. Using a combination of E. coli concentration, tidal phase, and antecedent rainfall, the first part of this dissertation focused on the combined assessment of quantitative-PCR (qPCR), FIB and environmental parameters to show the practicality of using MLR in a regulatory framework to provide estimates of water quality in estuaries, specifically impacted by tidal inundation. Additionally, recent advancements towards the implementation of a fecal indicator virus (FIV), coliphage, have also been proposed as a monitoring tool for use in fresh and marine surface waters. However, the utility of coliphage as an additional water quality management criterion has yet to be fully evaluated. Using US EPA developed protocols for quantification of somatic and male specific coliphage, the second focus of this work looked at the applicability of using such a fecal indicator virus into a monitoring framework by comparing relationships of coliphages with FIB and qMST approaches in surface waters with diffuse source pollution. It was determined that coliphage enumeration in this system proved to be cumbersome, and expensive and, as such, it is suggested that for surface water monitoring, it may be useful to focus on a combination of qPCR and FIB approaches to identify hot spots, and better quantify specific sources of human fecal contamination. Finally, watershed-scale drivers of fecal contamination were assessed in the context of qMST and FIB molecular markers with environmental parameters such as elevation, land use and land cover. Work here was conducted in an urban watershed within the Washington DC metropolitan area and detailed a prioritization of sites across the sampling landscape based on qMST and FIB marker concentrations most associated with risk. This study also incorporated the use of predictive modeling with the ultimate goal of the research being to provide coastal managers approaches that may be incorporated in future water quality monitoring program designs across vast geo-spatial scales.Doctor of Philosoph

Risk control in recycled water schemes

Recycled water is becoming one of the indispensable and reliable water resources at present. When it is introduced as an alternative source, risks on human health and the environment become major constraints driving the application and extension of recycled water. The authors examine the sources and associated risks of recycled water and introduce the practical risk control technologies on various end uses. They also review some existing risk assessment models by comparing their strengths and weaknesses toward the good approach of integrated modeling. Some critical suggestions on risk management and communication are made based on the given information. © 2013 Taylor and Francis Group, LLC

The Ecology of Fecal Indicators

Animal and human wastes introduce pathogens into rivers and streams, creating human health and economic burdens. While direct monitoring for pathogens is possible, it is impractical due to the sporadic distribution of pathogens, cost to identify, and health risks to laboratory workers. To overcome these issues, fecal indicator organisms are used to estimate the presence of pathogens. Although fecal indicators generally protect public health, they fall short in their utility because of difficulties in public health risk characterization, inconsistent correlations with pathogens, weak source identification, and their potential to persist in environments with no point sources of fecal pollution. This research focuses on characterizing the ecology of fecal indicators using both modeling and metabolic indicators to better understand the processes that drive fecal pollution. Fecal indicator impairment was modeled in Sinking Creek, a 303 (d) listed stream in Northeast Tennessee, using the ecological niche model, Maxent, for two different fecal indicators. While the use of Maxent has been well demonstrated at the macroscale, this study introduces its application to ecological niches at the microscale. Stream impairment seasonality was exhibited in two different indicators over multiple years and different resolutions (quarterly versus monthly sampling programs). This stresses the need for multiple year and month sampling to capture heterogeneity in fecal indicator concentrations. Although discharge is strongly associated with dissolved solutes, fecal indicator impairment was governed by other ecological factors such as populations of heterotrophic bacteria, enzyme activity, nutrient conditions, and other metabolic indicators. This research also incorporated metabolic indicators to characterize spatiotemporal variability in microbial community function, making connections to fecal and other pollution gradients. Communities differed in their ability to use a wide variety of substrates, and metabolic inhibition in sediments captured most of the interaction of aquatic and benthic communities. Sediment substrate activity was also indicative of degrees of pollution, suggesting that sediment is a potential reservoir for Escherichia coli in this stream, and there is possibility for resuspension, extended residence times, and increased duration for exposure. This research highlights the benefit of using models and other microbial indicators to better understand how environment shapes the niche of fecal indicators

The Application of Microbial Source Tracking to aid in Site Prioritization for Remediation in Lower Michigan

Non-point source fecal pollution is a threat to both the environment and public health. Climate change, aging infrastructure, and intensified agricultural practices are predicted to accentuate this issue. In Michigan, due to the high instance of aging infrastructure and intensified agriculture, non-point source fecal pollution has caused many waterbodies to exceed the state standards posing a risk to recreational activities and source water. Due to this threat, there is an increased effort to identify and remediate these sources. My study focused on improving the identification of non-point source fecal pollution through a combination of culture-based and molecular fecal indicator bacteria (FIB) identification, combined with geospatial and statistical modeling approaches. In Chapter 2, I assessed associations between measured FIB and key watershed characteristics in two watersheds located in Ottawa County, Michigan: Bass River and Deer Creek. Results indicated several associations between watershed characteristics and monitored FIB, which should be considered in future non-point source monitoring efforts. In Chapter 3, I created a new tool to aid stakeholders in interpreting FIB monitoring results. This tool was applied to FIB data from the previous chapter as well as FIB data from five public beaches in Macomb County, Michigan. Results indicated that the framework could improve the interpretation of monitored data. Using this tool, stakeholders can better identify and remediate the most impaired areas first, maximizing their impact and minimizing costs. In Chapter 4, I assessed potential improvements to components of a commonly used geospatial model, the Agricultural Conservation Planning Framework (ACPF), and looked at the model’s ability to assess non-point source fecal pollution from runoff derived events. To determine this, I first updated the sediment delivery ratio (SDR) in runoff risk and compared the updated outputs to measured FIB to identify ACPF’s ability to assess FIB concentrations. Results indicated a significant difference between model outputs, but limitations in experimental design precluded an adequate assessment of my objective for this chapter. Recommendations on future studies to properly assess these objectives were offered

Governance:Governance Frameworks for Wastewater Management

MVZ specimen catalog numbers and views represented. (XLSX 495 kb

Foodborne and Antibiotic Resistant Pathogens Prevalence During Fresh Produce Production Using Non-Traditional Water Sources: Fate, Transport, and Risk Assessment Study

A growing population and demand for food force agricultural leaders to look for alternative water sources. Wastewater reuse could be introduced into commercial operations, if regulations and measures are in place to ensure food safety. The objective of this project was to grow and irrigate lettuce with wastewater to track the fate of Escherichia coli and AP205 bacteriophage during and after cultivation to assess their fate and transport. Subsequently, quantitative microbial risk assessment (QMRA) was performed to estimate risk of illness to the public. Contamination levels in foliage, leachate, and soil were directly (P < 0.05) related to initial concentrations of microorganisms in the irrigation water. E. coli concentrations during post-harvest storage (14 days at 4 oC) of foliage increased by over 400%, while AP205 concentrations decreased more than 2 logs. From randomly selected E. coli colonies, in all four biomass types, 81% and 34% showed resistance to ampicillin and cephalothin, respectively. QMRA revealed significant health risks associated with lettuce consumption. E. coli concentrations were used as a fecal indicator bacteria to estimate levels of 6 common pathogens in wastewater and AP205 concentrations were used to estimate norovirus and rotavirus levels. Norovirus and Giardia largely contributed to the 0.8 probability of illness developing from infection, while norovirus and rotavirus showed a 0.24-0.43 probability of illness developing from infection, when using E. coli and AP205 concentrations, respectively. Results show that non-traditional water usage for fresh produce cultivation can pose risks to humans, if standards are not in place to control pathogen contamination levels

WATERBORNE ENTERIC VIRUSES AND COLIPHAGES - OCCURRENCE, SURVIVAL AND RISKS IN TROPICAL SURFACE WATERS

Ph.DDOCTOR OF PHILOSOPH

Sands and environmental conditions impact the abundance and persistence of the fecal indicator bacteria Enterococcus at recreational beaches

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2012The marine fecal indicator Enterococcus is measured at beaches to detect fecal contamination events, and beaches are closed to bathers when Enterococcus is found to exceed the federally mandated limit. This dissertation presents evidence that beach sands are an environmental reservoir of enterococci, tests the relationship between beach sand enterococci and water quality measurements, examines how real-time environmental conditions measured at beaches can be used to better understand and predict water quality violations, and uses molecular methods to provide an alternative characterization of water and sand fecal contamination. Initially, a qPCR method was developed and applied to monitor enterococci DNA in sands. Subsequently this qPCR method was used in tandem with traditional detection of culturable enterococci in sand and water at recreational beaches that have closures every summer. One field season was spent in Maine at beaches in the Wells National Estuarine Research Reserve, where high frequency water and weather measurements are routinely collected in situ. Two field seasons were spent at the beach in Provincetown Harbor, Massachusetts, where a weather station and ADCP were deployed to characterize the environmental conditions associated with observations of elevated enterococci. All studies revealed that environmental variables were related to the distribution of enterococci in sands and water, with water temperature and tides having the strongest relationship to enterococci in water. In dry weather, elevated enterococci in sands were strongly related to the increased moisture content of sands during spring tides. These environmental variables were used in multiple linear regressions to explain a significant amount of the variation observed in environmental enterococci abundance, which notably had no relationship to molecular markers of human fecal pollution. Results suggest that under certain conditions sands can contribute bacteria to the water and that tidal cycles, which are not taken into account in monitoring schemes, can bias routine sampling.This work was funded though a fellowship and student research grant from the Woods Hole Coastal Ocean Institute, as well as a grant through the Woods Hole Ocean Venture Institute. Thanks to WHOI Academic Programs for their support of my work in the Joint Program. Additionally, this research was supported by the National Science Foundation grant OCE- 0430724, and the National Institute of Environmental Health Sciences grant P50ES012742 to the Woods Hole Center for Ocean and Human Health

Estimating Associated Human Health Risk from Recreational Exposures in Fresh Water Bodies Impacted by Multiple Fecal Sources

Pathogens are the leading cause of impairment for rivers and streams in the United States. Microbial contamination in recreational water bodies was the cause of 510 waterborne disease outbreaks in the United States. Water quality standards should prevent these outbreaks from occurring, however, in 93% of outbreaks, where water quality information was available, the water body was meeting water quality standards at the time of the outbreak. The probability of gastrointestinal (GI) illness from recreational exposure to human, cattle, and wildlife fecal contamination was calculated in three water bodies impaired by microbial contamination by applying Quantitative Microbial Risk Assessment (QMRA) and Microbial Source Tracking (MST). Six reference pathogens were used to estimate the probability of GI illness: Campylobacter, Cryptosporidium, E. coli O157:H7, Giardia, norovirus, and Salmonella. The largest contributor of fecal contamination within the water bodies (wildlife) had the least significant impact on human health in all three water bodies. Whereas, human fecal sources had the most significant impact on the probability of GI illness, especially through the reference pathogen norovirus. Non-point source fecal loads were spatially estimated within the Lampasas River Watershed using SELECT from three general sources: cattle, human, and non-avian wildlife. SWAT was used to simulate source specific in-stream E. coli concentrations from the fecal loads estimated by SELECT. SWAT-simulated in-stream E. coli concentrations were used to estimate reference pathogen doses which were input into a QMRA to estimate human health risk associated with exposure to fecal contamination from contact recreation in impaired waters. Across all flow conditions, the WWTP had the most significant impact on human health risk even though it was not the largest contributor to fecal contamination. The probability of GI illness associated with the WWTP exceeded the acceptable GI illness rate but the WWTP was meeting water quality regulations. Water bodies are regulated by developing a total maximum daily load (TMDL) to determine the largest contributor of fecal contamination and make appropriate load reductions to that contributor. For regulation and remediation to have significant impacts, it should be focused on sources that are the riskiest to human health