Integrated Proteomics and Metabolomics Reveal Multifaceted Mechanisms of Colistin Resistance in Acinetobacter baumannii

Background: The emergence of colistin-resistant Acinetobacter baumannii , particularly extensively drug-resistant carbapenem-resistant A. baumannii (XDR-CRAB), poses a critical global health threat; however, the molecular mechanisms underlying this resistance remain poorly characterized. Methods: This study utilized integrated tandem mass tag (TMT)-based proteomics and untargeted metabolomics to compare a representative drug-sensitive (DS) strain, a colistin-sensitive multidrug-resistant (MDR-CRAB) strain, and a colistin-resistant extensively drug-resistant (XDR-CRAB) isolate from a Guangzhou hospital, China, with a primary focus on the molecular features associated with resistance in the XDR isolate. Results: Proteomic analysis identified 260 differentially expressed proteins (DEPs) across these strains, with 98 strongly linked to the colistin-resistant phenotype. These DEPs were enriched in functions related to polysaccharide and sulfate transport, aromatic compound degradation, and cationic antimicrobial peptide (CAMP) resistance. Upregulation of the lipid A modification system, driven by increased expression of PmrA (4.2-fold), PmrB (2.9-fold), and PmrC (5.5-fold) in the XDR strain compared to the MDR strain, is consistent with this CAMP resistance. Metabolomic analysis identified 747 metabolites, with lipids and lipid-like molecules being the most altered class. The XDR strain exhibited reduced relative abundance of several glycerophospholipids and fatty acids/conjugates, when compared to the MDR strain, indicating cell membrane remodeling. Pathway enrichment analysis further implicated purine, glycerophospholipid, starch/sucrose, and glutathione metabolism in colistin resistance. Conclusion: Colistin resistance in A. baumannii appears to involve a multifaceted strategy integrating lipid A modification, cell membrane remodeling, and metabolic reprogramming. This study provides a high-resolution molecular blueprint of colistin resistant A. baumannii and generates testable hypotheses to inform future diagnostic and therapeutic strategies against resistant infections. Keywords: Acinetobacter baumannii , multidrug-resistant, extensively drug-resistant, colistin, carbapenem, quantitative proteomics, untargeted metabolomics, lipid A modification