Nucleic Acid Measurements for Antibiotic Susceptibility Testing and Early Detection of SARS-CoV-2

Author: Savela, Emily Sue

Year: 2022

Degree: Dissertation (Ph.D.)

Advisor: Ismagilov, Rustem F.

Committee Members: Pierce, Niles A.; Newman, Dianne K.; Leadbetter, Jared R.; Ismagilov, Rustem F.

Option: Bioengineering

DOI: 10.7907/vp9a-n206

Abstract

Nucleic-acid-amplification tests (NAATs) are widely used in microbial detection both in environmental characterization and human diagnostics. NAATs offer highly sensitive and specific detection of target molecules among the noise of complex samples. This thesis covers two important applications of nucleic-acid quantification techniques in human clinical samples. First, I co-developed a new phenotypic antibiotic susceptibility test that uses species-specific DNA detection to detect bacterial cell-wall damage following incubation with beta-lactam antibiotics. Second, I helped compile a longitudinal dataset of SARS-CoV-2 viral loads during a community-based COVID-19 study run by the Ismagilov Lab through October 2020 – April 2021 in the greater Los Angeles County area, USA. Sensitive and specific nucleic-acid tests allowed for robust detection of pathogenic microbes in both these applications. Designing and implementing NAATs for these applications required consideration of biological constraints of the microorganisms, molecular stability over the time of quantification, and the practical constraints of acquiring and transporting samples. Continued innovation of NAAT technologies will be critical to contain present and future pandemics and empower medical professionals with data to inform treatment options.

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