Advisor(s)

Juan Calix

Committee Member(s)

Elliot Lefkowitz
Megan Kiedrowski
Sixto Leal
William Swords

Document Type

Dissertation

Date of Award

6-18-2026

Degree Name

Doctor of Philosophy (PhD)

School

Joint Health Sciences (Interdisciplinary)

Department

Microbiology

Abstract

Understanding the genomic structure of bacterial populations is essential for tracking antimicrobial resistance and informing public health strategies to prevent spread of multidrug resistant organisms. In this study, we investigated the diversity and distribution of carbapenem-resistant Acinetobacter baumannii (CRAb) lineages across a major healthcare system in the U.S. Deep South through both retrospective and prospective isolate collection. Our analysis revealed a heterogeneous population composed of multiple genotypically and phenotypically distinct lineages. To improve the resolution of lineage classification, we applied average nucleotide identity (ANI) as a high-resolution metric for comparative genomics. A ≥99% ANI threshold effectively delineated lineages, outperforming traditional multilocus sequence typing (MLST) by resolving subpopulations that were indistinguishable using single- or double-locus variants of MLST. Additionally, we extended this work to characterize Streptococcus pneumoniae genomes, successfully identifying lineage and capsule locus variation using the same pipeline. These findings demonstrate the utility of ANI for resolving bacterial population structure and support its use as a component of genomic surveillance systems. By establishing a reproducible method for lineage assignment, this work contributes to efforts aimed at improving diagnostic accuracy, outbreak detection, and the integration of genomic data into translational research on antimicrobial resistance.

Keywords

Acinetobacter baumannii;bacterial lineages;comparative genomics;molecular epidemiology

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