Molecular Characterization of Colistin Resistance Determinants in Clinical and Patient-Environmental Multidrug-Resistant Acinetobacter baumannii

Background Acinetobacter baumannii has emerged as an important nosocomial pathogen due to its multidrug resistance (MDR) and increasing resistance to colistin, one of the last-line therapeutic agents. Understanding the molecular mechanisms underlying colistin resistance is essential for effective antimicrobial stewardship and infection control. Methods A prospective hospital-based study was conducted between August 2023 and October 2024 and included 110 MDR A. baumannii isolates comprising 55 clinical and 55 environmental isolates recovered from patient surroundings. Colistin susceptibility was determined by broth microdilution (BMD) according to Clinical and Laboratory Standards Institute (CLSI) 2024 guidelines. Whole-genome sequencing was performed using the Illumina MiSeq platform. Genomic analyses were undertaken to identify plasmid-mediated mcr genes and chromosomal mutations associated with colistin resistance. Results Of the 55 clinical isolates, 43 (78.2%) were colistin susceptible and 12 (21.8%) were resistant, whereas 48 (87.3%) environmental isolates were susceptible and 7 (12.7%) were resistant. Most isolates exhibited a colistin minimum inhibitory concentration (MIC) of 1 mg/L. Plasmid-mediated mcr genes were identified in three clinical resistant isolates ( mcr-1 , n  = 2; mcr-4 , n  = 1) and one environmental resistant isolate ( mcr-1 , n  = 1). Chromosomal resistance mechanisms among clinical isolates included mutations in pmrA (M12I), pmrB (A138T and A444V), lpxD (E117K), and insertion of ISAba1 upstream of eptA/pmrC . A pmrB (T235I) mutation was detected in one environmental isolate. Five colistin-resistant isolates lacked identifiable plasmid-mediated or chromosomal resistance determinants, suggesting the involvement of alternative resistance mechanisms, including heteroresistance. Conclusions Colistin resistance among MDR A. baumannii was predominantly associated with chromosomal mutations rather than plasmid-mediated mcr genes. The detection of resistant isolates lacking known genetic determinants highlights the complexity of colistin resistance and suggests the presence of additional resistance mechanisms. Integrating phenotypic susceptibility testing with whole-genome sequencing can improve the detection and surveillance of colistin resistance and support antimicrobial stewardship and infection prevention strategies.