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


Savela, Emily Sue (2022) Nucleic Acid Measurements for Antibiotic Susceptibility Testing and Early Detection of SARS-CoV-2. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/vp9a-n206.


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.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:antibiotic resistance, sexually transmitted infection, diagnostics, antibiotic, Neisseria gonorrhoeae, COVID-19; Saliva; Nasal swab; Diagnostics; Pre-Symptomatic; Surveillance; RT-qPCR; Longitudinal sampling; Case-ascertained; Household study; Transmission
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Bioengineering
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Ismagilov, Rustem F.
Thesis Committee:
  • Pierce, Niles A. (chair)
  • Newman, Dianne K.
  • Leadbetter, Jared R.
  • Ismagilov, Rustem F.
Defense Date:22 October 2021
Funding AgencyGrant Number
Burroughs Wellcome FundIDSEP160030-02
Joan and Jerry Doren FellowshipUNSPECIFIED
Bill and Melinda Gates FoundationUNSPECIFIED
Ronald and Maxine Linde Center for New InitiativesUNSPECIFIED
Joseph J. Jacobs Institute for Molecular Engineering for MedicineUNSPECIFIED
Defense Threat Reduction Agency (DTRA)MCDC-18-01-01-007
Record Number:CaltechTHESIS:10072021-173853251
Persistent URL:
Related URLs:
URLURL TypeDescription adapted for Chapter II. adapted for Chapter III. adapted for Appendix A. adapted for Appendix B.
Savela, Emily Sue0000-0001-9614-4276
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:14388
Deposited By: Emily Savela
Deposited On:22 Nov 2021 18:24
Last Modified:30 Nov 2021 20:35

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