Theses and Dissertations from UMD
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Item METHOD VALIDATION AND DEVELOPMENT FOR THE METAGENOMIC EXPLORATION OF MICROBIAL COMMUNITIES(2022) Commichaux, Seth; Pop, Mihai; Rand, Hugh; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Our world is inhabited and shaped by diverse and complex microbial communities which we are only beginning to characterize and understand. With the advent of affordable high-throughput sequencing, the study of the genomic content of microbial communities, metagenomics, has accelerated our understanding of their impact on human and environmental health. The increasing number of datasets produced by metagenomic studies provide many opportunities for novel bioinformatic analyses and for the development of computational methods. However, careful benchmarking and validation are also important undertakings to ensure the integrity of methods and research in such a rapidly developing field. Here, we explored several problems in metagenomics by benchmarking existing methods and technologies, developing new methods, recommending best practices, and highlighting opportunities for future work. First, microbial gene catalogs document and organize the genes found in microbial communities and provide a reference for the standardized analysis of metagenomic data. Although commonly used to explore the intersection between microbiomes, humans, and ecosystems, the methods used for their construction and effectiveness for metagenomic analyses had not been critically evaluated. Our analysis highlighted important limitations of gene catalogs, opportunities for future research, and allowed us to recommend best practices. Second, we assessed if nanopore long read sequencing could expedite the accurate reconstruction of a pathogen genome from a microbial community. The investigation of foodborne illness outbreaks routinely uses short-read whole genome sequencing of pure culture pathogen colonies. However, culturing is a bottleneck and short reads cannot span all bacterial genomic repeats, often leading to fragmented assemblies. Our results showed that the integration of long-read sequencing could expedite the public health response by reconstructing complete pathogen genomes from a microbial community after limited culturing. Additionally, our evaluation of state-of-the-art assembly tools identified biases and areas for improvement. Third, we describe taxaTarget, a supervised learning approach for the taxonomic classification of microeukaryotes in metagenomic data. Metagenomics has been underutilized for microeukaryotes due to the many computational challenges they present. Existing tools often implement universal sequence similarity cutoffs which ignore that sequences can evolve at different rates and, thus, have different discriminatory power. We show that a data-driven approach to determining classification thresholds can result in higher sensitivity and precision than existing tools. Fourth, we explored the use of horizontally transferred plasmids to relate an outbreak strain to the microbiome of a suspected environmental source. The investigation of the 2020 red onion outbreak recovered the outbreak strain from patients but not the farms implicated as the likely source of contamination. Our analysis identified highly similar plasmids in the outbreak strain and environmental isolates collected from the farms, which supported a connection between the outbreak strain and the implicated farms. Additionally, we highlighted the need for more detailed and accurate metadata, more extensive environmental sampling, and a better understanding of plasmid molecular evolution before such analyses can be added to the public health response.Item SALMONELLA ENTERICA STRATEGIES FOR PERSISTENCE ON TOMATO (SOLANUM LYCOPERSICUM) AND SEROVAR DYNAMICS IN SURFACE AND RECLAIMED WATER(2019) Ferelli, Angela Marie Cecelia; Micallef, Shirley A.; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)While select aspects of Salmonella enterica subspecies enterica persistence in agricultural matrices have been illustrated, serovar specific survival strategies in surface water, transmission, and persistence on plants are multifaceted and remain only partially examined. In the present work, we utilized an interdisciplinary approach to illustrate novel mechanisms by which S. enterica may adapt to plants as an alternative host. Furthermore, we leveraged the wealth of diversity in S. enterica serovars to investigate specific dynamics and drivers of persistence in water and transfer onto produce crops. Through biochemical, gene expression, and plant challenge assays of both tomato (Solanum lycopersicum) vegetative and fruit organs, we found that plant-derived NO was generated in response to S. Newport recognition. Furthermore, bacterial gene expression on both leaves and fruit was indicative of adaptation to a novel environment including upregulation in NO detoxification machinery, indicating plant-derived NO as a novel bacterial stress. NO tolerance of various S. enterica was then evaluated to investigate drivers of “produce associated’ S. enterica adaptation to the plant niche. We identified that plant derived NO can negatively affect titers of all S. enterica serovars tested and that serovar specific tolerance to NO in vitro was apparent in a concentration and exposure time dependent manner. Finally, the survival of various S. enterica in surface and reclaimed water was investigated while evaluating the potential for transition to viable but non-culturable (VBNC) organisms. Furthermore, surface water used for irrigation, a common water environment for S. enterica, was investigated as a priming reservoir for various S. enterica serovars for enhanced transmission onto tomato crops. Persistence in water included VBNC subpopulations and was driven by water type. Transfer success onto tomato was driven by serovar, and prolonged incubation in water increased the transfer ability of serovars that initially transferred poorly onto tomato. Finally, attachment to polystyrene and water oxidation-reduction potential were identified as possible indicators of foodborne pathogen transfer success onto tomato. Moving forward, a greater understanding of the environmental queues used by S. enterica subspecies enterica responding to the agricultural environment will aid researchers in developing S. enterica targeted on-farm management techniques to ensure safe yet sustainable fresh produce cultivation practices.Item ESSAYS ON QUALITY CERTIFICATION IN FOOD AND AGRICULTURAL MARKETS(2017) Adalja, Aaron Ashok; Houde, Sebastien; Agricultural and Resource Economics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This dissertation features three essays exploring the market impacts of two types of quality certification---a voluntary non-GMO label and a mandatory food safety standard. In the first essay, I use a hedonic framework to examine whether firms use a voluntary quality certification for non-GMO products to extract rent from customers. Using U.S. retail scanner data coupled with data from a voluntary non-GMO label, I find no evidence of price premiums or quantity changes for newly certified non-GMO products. Instead, the label may induce firms to develop new non-GMO products targeted to high-valuation consumers. The second essay examines how voluntary non-GMO food labeling impacts demand in the ready-to-eat [RTE] cereal industry. I estimate a discrete-choice, random coefficients logit demand model using monthly data for 50 cereal brands across 100 DMAs. Consumer tastes for the label are widely distributed, and this heterogeneity plays a substantial role in individual choices; but, on average, the non-GMO label has a positive impact on demand. I estimate welfare effects by simulating two labeling scenarios: one in which all brands use the non-GMO label, and one in which no brands use the label. The simulation results suggest that non-GMO labeling in the RTE cereal industry may improve consumer welfare on average. In the final essay, we use data from an original national survey of produce growers to examine whether complying with the Food Safety Modernization Act's Produce Rule will be prohibitively costly for some growers. We examine how food safety measure expenditures required by the Rule vary with farm size and practices using a double hurdle model to control for selectivity in using food safety practices and reporting expenditures. Expenditures per acre decrease with farm size, and growers using sustainable farming practices spend more than conventional growers on many food safety practices. We use our estimates to quantify how the cost burden of compliance varies with farm size. We also explore the policy implications of exemptions to the Rule by simulating how changes to exemption thresholds might affect the cost burden of each food safety practice on farms at the threshold.Item Food Product Recalls: Trends and Demand Impacts(2016) Tselepidakis, Elina; Lichtenberg, Erik; Agricultural and Resource Economics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Food product recalls, the removal of risky food products from the marketplace, can impose significant burdens for consumers, producers, and regulators. The purpose of this dissertation is to offer an in-depth investigation of the trends and demand impacts of food product recalls. The first objective is to analyze trends and patterns of food product recall events from 2004 to 2013. The analysis considers multiple factors, including the types of foods being recalled, the reasons for initiating the recalls, the severity of the risks posed by the recalled products, and the geographic distribution. The second objective is develop a general Bayesian model to illustrate how consumers form perceptions of risk based on personal experiences and external signals, such as recall events. The model illustrates frequently observed behavior following the release of negative information: an immediate change in behavior, followed by a gradual return to previous, routine behavior. The third objective is to estimate the impact of leafy green recall events on the demand for packaged leafy green products by analyzing disaggregated household purchasing data. The results of this analysis suggests that iceberg and romaine recall events negatively impacted demand for the implicated leafy green in the weeks immediately following the recall. The fourth objective is to estimate the impact of STEC-contaminated ground beef recall events on the demand for ground beef products, differentiating between recalls prompted by consumer illness investigations and those prompted by laboratory testing. The results suggest that the impacts of recalls prompted by consumer illnesses outbreaks were often greater in magnitude and lasted longer than the impacts of recalls prompted by pathogen testing.Item DEMAND FOR SAFER FOOD IN DEVELOPING COUNTRIES(2016) Ordonez, Romina Valeria; Hoffmann, Vivian E; Agricultural and Resource Economics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)According to the WHO, in less developed countries approximately 2.2 million people—most of whom are children—die annually of food and waterborne diseases. In these economies, information on the safety attributes of food is usually not available and enforcement of food safety regulations is often weak, particularly within markets for locally consumed food. Still, food safety in the developing world has long been considered a secondary concern relative to food availability. The goal of this dissertation is to contribute to a deeper understanding of some of the constraints that surround demand for safer food along food supply chains in developing countries. Consumers’ demand for safe food can be thought of as an investment in preventive health, which has been shown to be extremely low in developing countries. Hence, this dissertation contributes to the economics literature that explores the impact of health-related information on preventive health behaviors in poor countries. This dissertation focuses on the role of food safety information in affecting people’s purchase behavior in a developing country setting. Because food safety is mostly a credence attribute that cannot be ascertained—or is too costly to ascertain—even after consumption, the provision of information has an important role to play in the reduction of information asymmetries inside the food chains. Among the several actors that are involved in food value chains, this dissertation focuses on small-scale informal intermediaries and consumers. The effect of information on these actors’ demand for safer food is assessed through the estimation of willingness to pay for food labeled as having safer characteristics, and through the analysis of the effect of different types of health-related information on the decision of whether or not to purchase food advertised as safer to eat. To achieve this, two field experiments using revealed preference methods were conducted in Kenya, where maize, the staple food, is frequently contaminated with aflatoxin, a naturally-occurring fungal toxin that is harmful to human health. A brief introductory chapter is followed by a comparison of the advancement of food safety policy and research in developed countries with the corresponding evolution in developing countries (Chapter 2). The framed field experiment described in Chapter 3 tests whether maize traders in informal markets are willing to pay more for higher quality and safer maize. 369 traders from different markets across Kenya participated in a second-price sealed-bid auction in which information on moisture content and aflatoxin contamination of maize auctioned was varied experimentally using labels. The results show that information on moisture content significantly affects traders’ willingness to pay and suggest the observability of moisture content is limited. Also, the effect of information does not appear to be driven by the possibility of selling drier maize to the formal sector, nor by the intention to keep the dryer maize for own family consumption. Further, the impact of providing traders with information on aflatoxin contamination is over twice as large as the effect of moisture content information. These results show that there is potential for strengthening the price-quality relationship within this context by increasing the availability of information on maize quality and safety. Chapter 4 presents the results of a field experiment conducted among customers of small retail shops in Nairobi and smaller urban centers in eastern Kenya. Packages of maize flour were tested for aflatoxin, labeled as safe to eat when they complied with the aflatoxin regulation, and offered for sale at a 20% premium above the price of untested maize. Information messages about the health consequences of aflatoxin exposure and about local contamination prevalence were randomly varied across customers as they entered the shops. The results show that the impact of health messaging on purchase of tested maize varies significantly depending both on the specific content of the message, and on the characteristics and prior beliefs of consumers. Information on the local prevalence of aflatoxin contamination, which exceeded the vast majority of customers’ contamination priors, had the strongest impact on demand. This study demonstrates that combining information on the prevalence of a risk with its health consequences is an effective approach for encouraging preventive health behavior.Item MICROBIOLOGICAL ASSESSMENT OF ORGANIC PRODUCE PRE- AND POST- HARVEST ON MARYLAND FARMS AND IMPACT OF GROWING AND HANDLING METHODS ON EPIPHYTIC BACTERIA(2014) XU, Aixia; Buchanan, Robert L; Micallef, Shirley A; Food Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Although the consumption of organic produce has dramatically increased in recent years and many outbreaks continue to occur, the microbiological safety of organic produce has not been fully assessed. This study generated microbiological data to evaluate organic produce safety and also assessed the impact of growing methods (ground cover effects) and handling methods (washing practices) in organic lettuce systems. The study evaluated microbiological safety of pre- and post-harvest fresh produce samples from small organic farms in Maryland, the effect of mulching on survival of indicator bacteria and the impact of post-harvest washing method on microbiological safety and epiphytic bacterial communities. Results indicate that (1) washed post-harvest produce had higher risks than unwashed and pre-harvest organic produce as measured by indicator bacteria E. coli, total coliforms, APC, yeast and mold; (2) different mulches affected the microbial levels differently; (3) different washing methods altered the bacterial communities both immediately and following 5 days of storage. This study presents data that could be used to assess food safety risks of organic produce associated with their cultivation and on-farm handling practices.Item Isolation and characterization of antimicrobial resistant Staphylococcus aureus in retail ground meats(2010) Li, Yi; Meng, Jianghong; Food Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Staphylococcus aureus is commonly present in humans and animals. It can cause a variety of suppurative infections, food intoxication and toxic shock syndrome. Antimicrobial resistant S. aureus, especially methicillin-resistant S. aureus (MRSA), have emerged and are a major public health concern. There is an increasing risk of food production animals serving as a reservoir and transmitting S. aureus and MRSA in community environments. Due to the increased food safety risk posed by MRSA in addition to its multidrug resistance, we were interested in determining the prevalence of S. aureus and MRSA in retail meat and investing the multidrug resistance of the S. aureus isolates. A survey study was conducted, involving 480 retail ground meat samples (231 ground pork and 249 ground beef) collected in the Washington DC area from March 2009 to March 2010. Approximately 42.08% (n = 202) of the samples were identified as S. aureus positive and one MRSA isolate was recovered from a ground beef sample. Antimicrobial resistance testing showed 53.34% of recovered S. aureus isolates exhibited different levels of antimicrobial resistance to CLI, CHL, GEN, LEVO, CIP, SYN and TGC. The MRSA isolate was resistant to 8 of 22 antimicrobials tested. PFGE fingerprinting identified the MRSA isolate as USA300 subtype, which also carried genes of virulence factors PVL and protein A. Our findings indicated that antimicrobial resistant S. aureus strains were common in retail ground beef and port, and that MRSA could also be present in such products that could potentially serve as a reservoir.Item Detection of norovirus and indicator organisms on fresh produce(2005-12-06) Williams, Karen Elizabeth; Meng, Jianghong; Food Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Food borne illness is a major problem around the world. Recently, more food borne outbreaks involve produce as the vehicle and viruses as the source of contamination. Norovirus is a common food borne viral pathogen. Genetic diversity among the viruses has made detection difficult. Due to the difficulties in detection, the norovirus is an ideal candidate for having an indicator organism. FRNA bacteriophages share several similarities with enteric viruses and would be an ideal candidate. In this study, we evaluated reverse transcriptase polymerase chain reaction (RT-PCR) detection of norovirus and evaluated using FRNA bacteriophages, E. coli, and Enterococcus as indicator organisms for the virus on produce. Of the five RT-PCR methods tested, only two worked with both controls. Of the 180 produce samples tested, 37.2% were positive for FRNA bacteriophage, 17.2% were positive for Enterococcus, and 0% were positive for E. coli. We conclude that RT-PCR is not an efficient method for screening norovirus on produce and including FRNA bacteriophages as indicator organisms for viruses may help decrease outbreaks.