Macrophage-mediated antibiotic evasion and competitive dominance of mcr-3-carrying Escherichia coli

Mobile colistin resistance (mcr) genes compromise the efficacy of last-resort polymyxin antibiotics. Notably, the global prevalence of mcr-3 has continued to increase despite reductions in colistin use, suggesting that selective forces beyond direct antibiotic pressure contribute to its persistence. Here, mcr-3-positive Escherichia coli is shown to confer a survival advantage by reprogramming macrophage immunity. MCR-3-mediated lipid A modification blunted TLR4-NF-κB signaling, suppressed macrophage reactive oxygen species generation, and delayed phagosome-lysosome fusion, allowing mcr-3-positive strains to evade intracellular killing. Integrated transcriptomic and metabolomic analyses revealed extensive immunometabolic rewiring in infected macrophages, including altered glycerophospholipid and energy metabolism. Consistently, mcr-3 enhanced bacterial tolerance to ferrous iron stress, likely mitigating host-induced ferroptotic damage. In a mouse co-infection model, mcr-3-positive strains outcompeted isogenic negative strains under antibiotic treatment without differing in in vitro susceptibility, indicating that immune evasion rather than intrinsic drug resistance alone drives their competitive advantage. These findings reveal a dual mechanism where mcr-3 confers both antimicrobial resistance and immune suppression, enabling persistence under antibiotic pressure and highlighting the threat of mcr-3 dissemination independent of polymyxin use.