UMD Theses and Dissertations
Permanent URI for this collectionhttp://hdl.handle.net/1903/3
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 given thesis/dissertation in DRUM.
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Item Algorithms for scalable and efficient population genomics and metagenomics(2022) Javkar, Kiran Gajanan; Pop, Mihai; Computer Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Microbes strongly impact human health and the ecosystem of which they are a part. Rapid improvements and decreasing costs in sequencing technologies have revolutionized the field of genomics and enabled important insights into microbial genome biology and microbiomes. However, new tools and approaches are needed to facilitate the efficient analysis of large sets of genomes and to associate genomic features with phenotypic characteristics better. Here, we built and utilized several tools for large-scale whole-genome analysis for different microbial characteristics, such as antimicrobial resistance and pathogenicity, that are important for human health. Chapters 2 and 3 demonstrate the needs and challenges of population genomics in associating antimicrobial resistance with genomic features. Our results highlight important limitations of reference database-driven analysis for genotype-phenotype association studies and demonstrate the utility of whole-genome population genomics in uncovering novel genomic factors associated with antimicrobial resistance. Chapter 4 describes PRAWNS, a fast and scalable bioinformatics tool that generates compact pan-genomic features. Existing approaches are unable to meet the needs of large-scale whole-genome analyses, either due to scalability limitations or the inability of the genomic features generated to support a thorough whole-genome assessment. We demonstrate that PRAWNS scales to thousands of genomes and provides a concise collection of genomic features which support the downstream analyses. In Chapter 5, we assess whether the combination of long and short-read sequencing can expedite the accurate reconstruction of a pathogen genome from a microbial community. We describe the challenges for pathogen detection in current foodborne illness outbreak monitoring. Our results show that the recovery of a pathogen genome can be accelerated using a combination of long and short-read sequencing after limited culturing of the microbial community. We evaluated several popular genome assembly approaches and identified areas for improvement. In Chapter 6, we describe SIMILE, a fast and scalable bioinformatics tool that enables the detection of genomic regions shared between several assembled metagenomes. In metagenomics, microbial communities are sequenced directly without culturing. Although metagenomics has furthered our understanding of the microbiome, comparing metagenomic samples is extremely difficult. We describe the need and challenges in comparing several metagenomic samples and present an approach that facilitates large-scale metagenomic comparisons.Item Antimicrobial Resistance of Salmonella and E. coli from Pennsylvania Dairy Herds(2015) Cao, Huilin; Pradhan, Abani K.; Food Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The emergence and dissemination of bacterial antimicrobial resistance has become a major public health concern. A total of 444 manure composite samples were collected from 80 dairy farms in Pennsylvania, representing pre-weaned calves, post-weaned calves, dry cows, and lactating cows. E. coli and Salmonella were isolated, and tested for antimicrobial susceptibility. Salmonella was isolated from at least one sample from 51 (64%) farms and was more prevalent in adult animals than young animals. The predominant serotypes were Cerro, Montevideo and Kentucky. Salmonella isolates were mostly susceptible to all antimicrobials. E. coli were commonly resistant to tetracycline, streptomycin, sulfisoxazole and ampicillin. Resistance of up to 8 classes of antibiotics was observed in E. coli isolated from young animals. The blaCMY- and blaCTX-M-carrying E. coli were detected in 35% and 5% of the farms, respectively. The presence of multi-drug resistant E. coli suggested potential risks to human health associated with dairy farming.Item ANTIMICROBIAL RESISTANCE OF LISTERIA MONOCYTOGENES AND ENTEROCOCCUS FAECIUM FROM FOOD AND ANIMAL SOURCES(2005-12-07) Zhang, Yifan; Meng, Jianghong; Food Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The widespread use of antimicrobials in human and veterinary medicine, as well as in animal production has accelerated the development of drug resistance in a variety of pathogenic bacteria. Listeria monocytogenes and Entercoccus faecium are important Gram-positive pathogens of food safety and public health concern. But their mechanisms of antimicrobial resistance are relatively less clear than those in Gram- negative pathogens. L. monocytogenes (n=167) recovered from deli meats, conventional and organic chicken, and conventional and organic fresh produce samples were characterized by serogrouping, DNA fingerprinting and antimicrobial susceptibility testing. The isolates belonged to five different serogroups. Percentages of resistance to ciprofloxacin, tetracycline, sulfonamide, and nalidixic acid were 1.8%, 9%, 73%, and 100%, respectively. The identification of potential serotype 4b from all food categories, especially from organic chicken products, raised a public health concern, because serotype 4b has been the number one serotype associated with clinical isolates. Multiresistant L. monocytogenes strains were recovered from the food supply, including organic food products, suggesting our food supply may serve as the reservoir for multiresistant L. monocytogenes and the resistance genes. The PFGE and serogroup data also suggest the diverse sources of contamination. E. faecium isolates (n=34), including 33 from seven poultry farms and one from an outpatient in Michigan, were studied by characterizing the quinupristin-dalfopristin (Q/D) resistant plasmids that carried vatE. Hybridization following restriction endonuclease digestion identified five different plasmid types. The vatE-carrying plasmid from the human isolate showed nearly identical hybridization patterns, following restriction endonuclease digestion, to a vatE carrying plasmid from an E. faecium recovered from a chicken farm. This study showed that a heterogeneous group of plasmids harbour vatE in a heterogeneous population of E. faecium . Some of the plasmids were obtained by E. faecium capable of infecting humans. Q/D resistant E. faecium (n=28) with the MICs (minimal inhibitory concentrations) = 32 ug/ml were characterized by gene identification, conjugation, transformation, and in vitro transposon mutagenesis. vatE and ermB are responsible for high streptogramin resistance in most E. faecium isolates from poultry products but that the mechanisms of Q/D resistance among E. faecium isolates from poultry farms remain largely uncharacterized.