A Genomic and Proteomic Survey of Traits that Modulate Antimicrobial Resistance in Staphylococcus aureus

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Antibiotic resistance is a growing global public health crisis which threatens to remove our primary treatment against bacterial infections. The mechanisms of antibiotic resistance in bacterial pathogens have been extensively studied, however questions surrounding the regulatory mechanisms of these resistance factors in clinical isolates are yet to be answered. In collaboration with the Broad Institute of MIT and Harvard, The Harvard T.H. Chan School of Public Health, and Alberta Precision Laboratories we completed whole-genome sequencing on 7,997 Staphylococcus aureus genomes from a larger study cohort of over 38,000 blood stream infections over a 16-year period. In addition to whole-genome sequencing, the proteomes of the bacterial isolates were quantitatively assessed using Tandem Mass Tag (TMT) ultra-high-performance liquid chromatography mass-spectrometry (UHPLC-MS) methods. Changes in protein levels and growth in the bacterial isolates are related to the variability in the genetic composition of the resistance operons of the specific clinical strains. This study has resulted in the understanding of a complex coregulatory interaction between two resistance operons of Methicillin Resistant S. aureus related to the mecA and blaZ resistance factors. Further, to better understand the metabolic adaptations of pathogens under antibiotic exposure, kinetic flux profiling of Escherichia coli metabolism under various antibiotic stressors was completed through the addition of fully labelled 13C-glucose. This intracellular flux monitoring via UHPLC-MS analysis, at a scale of seconds, has been used to gain insight into the metabolic alterations within E. coli metabolism under the exposure to twelve antibiotics spanning three common classes of antibiotics: DNA synthesis inhibitors, protein synthesis inhibitors, and cell wall synthesis inhibitors. This study has resulted in the classification of important metabolic adaptations occurring because of specific antibiotic compounds. Further, this intracellular metabolic study has shown evidence of a previously unexpected mevalonate pathway in E. coli. These studies have provided insight into the dynamics of pathogen interactions with antibiotics, and a deeper understanding of the antibiotic resistance mechanisms existing in pathogenic strains.
MacKenzie, C. C. (2024). A genomic and proteomic survey of traits that modulate antimicrobial resistance in Staphylococcus aureus (Doctoral thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.