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

Ling Hao,1,2 Xiao Yang,3 Nadeem Ullah,4 Yujun Li,1 Shuquan Wei,1 Qizhi Wang,1 Zhuxiang Zhao,1 Zhike Liang1 1Department of Pulmonary and Critical Care Medicine, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, People’s Republic of China; 2Institute of Clinical Medicine, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, People’s Republic of China; 3Department of Laboratory Medicine, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, People’s Republic of China; 4Department of Clinical Microbiology, UmeÃ¥ University, UmeÃ¥, SwedenCorrespondence: Zhuxiang Zhao, Email [email protected] Zhike Liang, Email [email protected]: 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