摘要:SummaryRecent discoveries indicate that tolerance and resistance could rapidly evolve in bacterial populations under intermittent antibiotic treatment. In the present study, we applied antibiotic combinations in laboratory experiments to generate novel methicillin-resistantStaphylococcus aureusstrains with distinct phenotypes (tolerance, resistance, and suppressed tolerance), and compared their proteome profiles to uncover the adaptation mechanisms. While the tolerant strains have very different proteomes than the susceptible ancestral strain, the resistant strain largely resembles the ancestral in terms of their proteomes. Our proteomics data and other assays support the connection between the detected mutations to the observed phenotypes, confirming the general understanding of tolerance and resistance mechanisms. While resistance directly counteracts the action mechanism of the antibiotic, tolerance involves complex substantial changes in the cells’ biological process to achieve survival advantages. Overall, this study provides insights into the existence of diverse evolutionary pathways for tolerance and resistance development under different treatment scenarios.Graphical abstractDisplay OmittedHighlights•Laboratory evolution led to strains with distinct tolerance/resistance phenotypes•DAP/RIF combination applied to a DAP-tolerant strain increases its susceptibility•Protein network of DAP-tolerant strain is more perturbed than the resistant strain•Novel tolerance-related proteins revealed by proteomicsMicrobiology; Evolutionary biology; Proteomics