Development And Application Of Targeted Dna Sequencing Tools To Profile Microbiome-Wide Antimicrobial Resistance And Pathogens Of Public Health Importance
2024-02
Loading...
View/Download File
Persistent link to this item
Statistics
View StatisticsJournal Title
Journal ISSN
Volume Title
Title
Development And Application Of Targeted Dna Sequencing Tools To Profile Microbiome-Wide Antimicrobial Resistance And Pathogens Of Public Health Importance
Authors
Published Date
2024-02
Publisher
Type
Thesis or Dissertation
Abstract
Antimicrobial resistance (AMR) poses critical health challenges as drivers of frequent and severe global outbreaks. In the U.S. alone, AMR accounts for one infection every eleven seconds, and one death every fifteen minutes. Bacterial antimicrobial resistance genes (ARGs) are the underpinning determinants of AMR, and traditionally prevention and surveillance efforts have focused on cultivating and studying resistant pathogens harboring DNA-encoded ARGs, isolated from human, animal, food, and environmental sources. However, across most compartments of the biosphere, bacteria reside as community members of complex microbial ecosystems with diverse ecological interactions and defined niche profiles. The perspective of the community-level composition and processes that lead to AMR rise and dissemination is rarely accounted for. Though culture-independent methods like PCR have been used for decades, recent advances in the field of metagenomics offers the possibility of directly sequencing the entire genetic milieu across the total microbiota within a sample (i.e. the ‘metagenome’). This technique offers an ecosystem-wide glimpse into bacterial community members, their genes, and their functional potential. However, metagenomic sequencing is rarely adopted in public health surveillance and tracking of pathogens, as well as risk assessment of AMR. The resulting sequencing data offers a low resolution and fragmented view of AMR hazard potential within microbial communities which is not conducive to motivating quality evidence-based decision-making for clinicians, public health practitioners, food producers, and policy makers. This dissertation consists of four integrated studies that attempt to: (1) Formalize the major impediments precluding informative metagenomic sequencing and data analysis in the study of AMR and its hazard potential; (2) Demonstrate an improved metagenomic approach to elucidate epidemiological trends in a major public health context of AMR; (3) Innovate and implement a novel metagenomic sequencing platform and associated bioinformatic tools to address impediments to metagenomic sequencing and enhance risk characterization of AMR; and (4) Extend technical metagenomic innovations for deployment in public health surveillance and monitoring activities. All metagenomic methods involved the use of unique human, animal, environmental, and food safety-related samples, and all studies were conducted using systems in vivo, in vitro, and / or in silico.
Description
University of Minnesota Ph.D. dissertation. February 2024. Major: Veterinary Medicine. Advisors: Noelle Noyes, Jeffrey Bender. 1 computer file (PDF); xviii, 336 pages.
Related to
Replaces
License
Collections
Series/Report Number
Funding information
Isbn identifier
Doi identifier
Previously Published Citation
Suggested citation
Slizovskiy, Ilya. (2024). Development And Application Of Targeted Dna Sequencing Tools To Profile Microbiome-Wide Antimicrobial Resistance And Pathogens Of Public Health Importance. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/264366.
Content distributed via the University Digital Conservancy may be subject to additional license and use restrictions applied by the depositor. By using these files, users agree to the Terms of Use. Materials in the UDC may contain content that is disturbing and/or harmful. For more information, please see our statement on harmful content in digital repositories.