Associate Professor Arkady Khodursky

CBS Biochemistry
College of Biological Sciences
Twin Cities
Project Title: 
Systematic Identification of Targets for Antibiotic Adjuvants in Resistant Bacteria

Antibiotic resistance is widely recognized as a global public health threat, to which an effective response has become a critical clinical as well as societal objective. Since the emergence of resistance is the inevitable consequence of natural selection in antibiotic-containing environments, any new antibiotic's success will only be temporary. Such inevitability calls for development and implementation of strategies to preserve the utility of existing and future antibiotics. One such strategy is based on the use of antibiotic adjuvants, a broad class of compounds that includes those that can improve the efficacy of existing antibiotics by directly interfering with resistance mechanisms. This research addresses current critical shortcomings in the identification of adjuvant targets.

At present, adjuvant targets are discovered in genome-wide screens of genes whose inactivation (or overexpression) makes bacteria more antibiotic-susceptible. Such screens are done using model laboratory strains of wild-type bacteria. However, this group recently showed that assays utilizing wild-type, drug-susceptible bacteria do not correctly determine either the spectrum of putative targets or the magnitude of their effect on resistance. This stems from un-accounted for changes in the physiology and regulation of resistant bacteria. Furthermore, target-centric discovery of antimicrobial compounds has been significantly hampered by the difficulty of translating leads from biochemical assays into activity against whole cells. These researchers speculated that this is due in part to a singular focus on gene product functionality, without considering the significance of target abundance.

This project will address this shortfall in a target-based search for antibiotic adjuvants by accomplishing two specific aims: 1) Determine the set of adjuvant targets for fluoroquinolones and extended spectrum cephalosporins and the size of the effects of target genes on resistance in clinical Escherichia coli isolates. The researchers will use a strain from the H30 subclone of sequence type 131 (ST131-H30Rx) of extra intestinal pathogenic E. coli (ExPEC), which is fluoroquinolone-resistant, carries extended-spectrum β-lactamase (ESBL) genes, and has emerged as a dominant ExPEC lineage in humans. 2) Estimate protein abundances in ST131-H30Rx cells during steady-state growth and relevant physiological transitions. Since all known antibiotic targets are relatively abundant, the researchers will identify genes in the pathogen’s genome that encode for candidate adjuvant targets and rank them according to copy number. They will predict abundances from absolute protein synthesis rates by ribosome profiling using steady-state cultures, and will confirm the predictions by quantitative mass spectrometry. Completion of both aims will help develop rational approaches to foiling the resistance.

Project Investigators

Associate Professor Arkady Khodursky
Lev Ostrer
Professor Cavan Reilly
 
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