Omics analysis of MRSA under antibiotic stress identifies conserved adaptive modules and candidate adjuvant targets

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) survives antibiotic exposure through coordinated physiological adaptation that extends beyond canonical resistance determinants. Here, we used an untargeted multi-omics strategy integrating proteomics, post-translational modifications, and metabolomics to characterize MRSA ATCC 43300 responses to five mechanistically distinct antibiotics: ampicillin, methicillin, vancomycin, chloramphenicol, and ciprofloxacin. Cells were exposed to 0.5x, 1x, and 2x IC50, enabling comparison of graded stress responses across antibiotic classes. Across treatments, MRSA did not deploy fully distinct drug-specific programs. Instead, antibiotic exposure repeatedly converged on a limited set of conserved adaptive modules detectable across independent molecular layers. These included coupling of envelope stress with genome maintenance, recurrent remodeling of metal/cofactor and redox homeostasis, sustained pressure on nucleotide and folate metabolism, and reprogramming of transport and surface-associated functions. A particularly robust cross-antibiotic signature was the accumulation of MoO2-molybdopterin cofactor. Ciprofloxacin additionally induced compensatory envelope reinforcement, supporting tight coupling between DNA damage responses and cell-envelope maintenance. Overall, the data support a unified model in which MRSA buffers mechanistically distinct antibiotic stress through a compact set of conserved stress-response functions rather than through entirely separate adaptive programs. These recurrent modules highlight candidate adjuvant vulnerabilities, particularly in metal/cofactor handling, nucleotide supply and repair, and transport/envelope compensation pathways. As this was an exploratory design intended to identify candidate adaptive patterns, these vulnerabilities now require validation in biologically replicated cultures and targeted functional studies.