Theses and Dissertations from UMD
Permanent URI for this communityhttp://hdl.handle.net/1903/2
New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a give thesis/dissertation in DRUM
More information is available at Theses and Dissertations at University of Maryland Libraries.
Browse
4 results
Search Results
Item FOOD SAFETY IN THE ERA OF NEXT-GENERATION SEQUENCING: GENOMIC CHARACTERIZATION OF SHIGA TOXIN-PRODUCING ESCHERICHIA COLI AND METAGENOMIC SURVEILLANCE OF IRRIGATION SURFACE WATER(2023) Huang, Xinyang; Meng, Jianghong; Food Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In this study, we first utilized high-throughput next-generation sequencing (NGS) and bioinformatic analyses to characterize potential public health threats posed by non-top-7 Shiga toxin-producing Escherichia coli (STEC). NGS allowed us to detect virulence (n = 46) and antimicrobial resistance (AMR) (n = 27) factors within the genomes of the STEC strains, to make genome-wide comparisons with published human clinical isolates, and to characterize three novel O-antigen gene clusters. We found that the distribution of 33 virulence genes and 15 AMR determinants exhibited significant differences among serotypes (P < 0.05), and that 47 strains were genetically related to human clinical strains inferred from a pan-genome phylogenetic tree. We secondly developed a web tool, PhyloPlus, that allowed users to generate customized bacterial and archaeal phylogenies, which can be incorporated into their own microbial community studies. We also utilized two public datasets (human microbiome, n = 60; fermented food metagenomes, n = 62) to illustrate how application of phylogeny improved our analyses. We showed that the integration of phylogenies introduced alternative phylogeny-based diversity metrics and allowed more conservative null model constructions, thereby reducing potential inflation of type I errors. Finally, we employed deep metagenomic shotgun sequencing, and our developed web tool, to investigate on a collection of 404 surface water samples collected from four regions in Latin America. We reported the high detection rates of pathogenic and contaminant bacteria in these samples, including Salmonella (29.21%), Listeria (6.19%), and E. coli (35.64%), necessitating the monitoring and proper treatment on these surface waters. We also described the regional differences in terms of sample taxonomic composition and the resistome, and further presented key factors that drove the separation patterns for each sampling region. We utilized recent metagenomic assembly and binning algorithms to report the construction of 1,461 de-replicated metagenome-assembled genomes (MAGs) that were of at least medium quality. The incorporation of the MAGs into the taxonomic classifier Kraken2’s database led to a 12.85% increase in classifiable sequence reads. Additionally, we conducted network analysis on AMR genes and the genus-level taxonomy, based on assembled contigs, to provide information to better understand the dynamics of the transferring of AMR genes.Item Diversity, dynamics, and dissemination of microbial communities in reclaimed and untreated surface waters used for agricultural irrigation(2019) Chopyk, Jessica; Sapkota, Amy R; Public and Community Health; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)High quality freshwater is a vital resource for sustaining agriculture and feeding a growing global population. Yet, due to increasing declines in groundwater, key food production regions across the world face uncertainty with regard to water availability. Nontraditional irrigation water sources, such as reclaimed water (advanced treated municipal wastewater) and untreated surface water (e.g. creeks, ponds, and brackish rivers), may contribute to sustainable solutions to conserve groundwater supplies. However, the microbial community composition and dynamics within these water sources are typically poorly characterized and comparative analysis of their microbial communities are rare. Using high-throughput, cultivation-independent sequencing methodologies, this dissertation research focused on three aims: 1) exploring the functional and taxonomic features of bacteria in nontraditional irrigation water sources; 2) assessing the bacterial and viral communities of agricultural pond water in relation to seasonality; and 3) describing the dynamics, composition, and potential dissemination of irrigation water microbiota from a freshwater creek to an irrigated field. The first aim was addressed through a broad investigation of bacteria within agricultural ponds, freshwater creeks, brackish rivers, and reclamation facilities. Through metagenomic-based analyses, features of the bacterial community, such as antimicrobial resistance genes (ARGs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) arrays, were found to vary by sampling date and specific site. For the second aim, agricultural pond water was sampled over two time periods and found to harbor diverse bacteria and bacteriophage species, the abundance and composition of which were influenced by factors characteristic of the pond’s topography and seasonality. For the final aim, samples from a creek used actively for agricultural irrigation, as well as samples of pre- and post-irrigated soil, were analyzed. ARGs and virulence factors were identified in the water and soil samples, with the majority being specific to their respective environment. Moreover, analyses of CRISPR arrays from the creek samples indicated the persistence of certain bacterial lineages, as well as specific interactions between creek bacteriophage and their hosts. Overall, this research improves scientific knowledge of bacterial and viral composition, dynamics, and interactions that can be utilized to assess the suitability and safety of nontraditional irrigation water sources.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 EVALUATION OF ANTIBIOTIC-RESISTANT BACTERIA IN TERTIARY TREATED WASTEWATER, RECLAIMED WASTEWATER USED FOR SPRAY IRRIGATION, AND RESULTING OCCUPATIONAL EXPOSURES(2010) Goldstein, Rachel Elizabeth Rosenberg; Sapkota, Amy R; Maryland Institute for Applied Environmental Health; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Occupational exposures to vancomycin-resistant Enterococcus (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) in reclaimed wastewater used for spray irrigation were evaluated. In 2009, wastewater was collected from a tertiary-treatment facility, and reclaimed wastewater, nasal and dermal swab samples from an irrigation site. Samples were evaluated for MRSA and VRE using standard methods, PCR, and susceptibility testing. MRSA and VRE were isolated from all wastewater samples except effluent. While wastewater MRSA isolates were multidrug resistant (98%), no MRSA was isolated in irrigation water or swabs. VRE was isolated in one irrigation water sample. Fewer irrigation workers were colonized with S. aureus (31%) compared to controls (46%), but they harbored more multidrug resistant S. aureus. This is the first study to 1) evaluate antibiotic-resistant bacteria (ARB) in U.S. reclaimed wastewater and resulting occupational exposures, and 2) detect MRSA in U.S. wastewater. The findings suggested that tertiary wastewater treatment effectively reduced MRSA and VRE.