Evolutionary trajectories determine feasibility of collateral sensitivity-based antibiotic treatment strategies in critical bacterial pathogens

The rise of antibiotic resistance among pathogenic bacteria necessitates innovative therapeutic strategies, such as collateral sensitivity where resistance to one antibiotic increases susceptibility to another. We explored the clinical relevance of collateral sensitivity through genetic engineering and experimental evolution in the six critical bacterial pathogens Escherichia coli , Salmonella Typhimurium , Klebsiella pneumoniae , Acinetobacter baumannii , Pseudomonas aeruginosa , and Staphylococcus aureus . Our analysis of E. coli showed that clinically relevant resistance mutations did not confer collateral sensitivity, but we were able to identify at least three novel classes of ciprofloxacin-resistance mutations that cause collateral sensitivity to multiple antibiotics. Further analysis showed that the development of collateral effects differed between the tested species. Collateral sensitivity to gentamicin developed during ciprofloxacin-resistance evolution in almost all tested species, but A. baumannii developed collateral resistance instead. P. aeruginosa consistently developed collateral sensitivity, suggesting its potential for targeted treatment strategies. These findings highlight the complexity of collateral effects and support its therapeutic potential in designing more effective antibiotic regimens.