Genotypic and Phenotypic Resistance Profiles of Invasive Acinetobacter baumannii Isolates at Bulgarian University Hospital

Acinetobacter baumannii is a formidable nosocomial pathogen responsible for severe hospital-acquired infections. This study aimed to investigate the relationship between genotypic and phenotypic resistance profiles in 36 non-duplicate invasive A. baumannii isolates collected at a tertiary care hospital in Bulgaria over a six-year period (2019–2024). Identification was performed by MALDI-TOF MS and PCR-based detection of blaOXA-51-like and gyrB. Antimicrobial susceptibility testing to ten agents was performed by gradient diffusion and broth microdilution, and selected resistance genes were detected by conventional PCR. Whole-genome sequencing of 17 representative isolates was conducted to confirm the resistance genotype–phenotype associations and perform MLST. Carbapenem resistance was detected in 34/36 isolates (94.4%), mediated by blaOXA-23-like (29/34) or blaOXA-72 (5/34). The armA gene associated with high-level resistance to all three aminoglycosides was identified exclusively in blaOXA-23-like-positive isolates (18/29). In armA-negative isolates, gentamicin and tobramycin MICs decreased markedly, whereas amikacin MICs remained elevated. In addition, minocycline MICs ≥ 8 mg/L were observed in the presence of armA. Seven distinct genotypic–phenotypic profiles were defined based on these gene–MIC associations. Resistome and phylogenetic analyses confirmed these relationships, with MLST assigning the isolates to established clonal lineages ST2 and ST636 (International Clone II). These findings support the use of targeted genes, such as armA, combined with phenotypic testing to guide empirical therapy and strengthen local surveillance of high-risk A. baumannii clones in hospital settings.