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Despite significant metabolomic perturbations, some pathogens had minimal or no significant changes in their proteome. Notably, trimethylamine metabolism was consistently altered across all species, suggesting its role in survival under antibiotic stress. Shared adaptive responses to chloramphenicol in <jats:italic>S. aureus<\/jats:italic> and <jats:italic>E. faecium<\/jats:italic> are related to translation, oxidative stress management, protein folding and stability, biofilm formation capacity, glycine metabolism and osmoprotection. Alterations in quaternary amines and trimethylamine metabolism suggest alternative nitrogen and carbon utilization pathways in response to antibiotic stress. In <jats:italic>S. aureus<\/jats:italic>, vancomycin suppressed metabolism, including D-alanine metabolism, and global regulators LytR, CodY and CcpA. 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