Comprehensive whole-genome sequencing reveals the resistome, virulome, and mobile genetic architecture of multidrug-resistant Acinetobacter baumannii.

Acinetobacter baumannii is a major cause of hospital-acquired infections and has emerged as a critical multidrug-resistant (MDR) pathogen with limited therapeutic options. In this study, two MDR clinical isolates from a tertiary care hospital in Chennai, India, selected based on their strong biofilm-producing capacity, were subjected to whole-genome sequencing (WGS) to characterize their resistome, virulome, and genomic features. Both isolates exhibited resistance to β-lactams, carbapenems, aminoglycosides, fluoroquinolones, and trimethoprim-sulfamethoxazole, while remaining susceptible to tigecycline and colistin. Genomic analysis identified key carbapenemase genes blaOXA-23, blaOXA-51, and blaOXA-144 along with additional resistance determinants including blaADC-76 and blaPER-7, aminoglycoside-modifying enzymes (ant(3″)-Ia and aph(6)), tetracycline resistance genes (tet(A), tet(B), and tet(R)), macrolide resistance gene msr(E), sulfonamide resistance gene sul1, and chloramphenicol efflux gene cmlA5. Fluoroquinolone resistance was associated with mutations in the quinolone resistance determining regions, including an S81L substitution in gyrA and multiple substitutions in parC. Virulence profiling revealed biofilm-associated genes, including bap and the pgaABC operon, along with genes linked to motility and metabolic fitness. Phylogenomic analysis showed close relatedness between the isolates and reference strains, and multilocus sequence typing (MLST) assigned both isolates to sequence type ST1051, indicating a shared clonal background. The genomes also harbored diverse mobile genetic elements, prophage regions, and siderophore-associated biosynthetic gene clusters, reflecting high genomic plasticity. Overall, this study highlights the coexistence of multiple resistance and virulence determinants in biofilm-forming MDR A. baumannii, emphasizing the importance of genome-based surveillance for monitoring high-risk strains in clinical settings.