Whole-Genome Sequencing of a Colistin-Resistant Acinetobacter baumannii Strain Isolated at a Tertiary Health Facility in Pretoria, South Africa

's ( ) growing resistance to all available antibiotics is of concern. The study describes a colistin-resistant isolated at a clinical facility from a tracheal aspirate sample. Furthermore, it determines the isolates' niche establishment ability within the tertiary health facility. An antimicrobial susceptibility test, conventional PCR, quantitative real-time PCR, phenotypic evaluation of the efflux pump, and whole-genome sequencing and analysis were performed on the isolate. The antimicrobial susceptibility pattern revealed a resistance to piperacillin/tazobactam, ceftazidime, cefepime, cefotaxime/ceftriaxone, imipenem, meropenem, gentamycin, ciprofloxacin, trimethoprim/sulfamethoxazole, tigecycline, and colistin. A broth microdilution test confirmed the colistin resistance. Conventional PCR and quantitative real-time PCR investigations revealed the presence of , , and , while was not detected. A MIC of 0.38 µg/mL and 0.25 µg/mL was recorded before and after exposure to an AdeABC efflux pump inhibitor. The whole-genome sequence analysis of antimicrobial resistance-associated genes detected beta-lactam: ; ; ; ; ; , and ; aminoglycoside: ; ; and and a colistin resistance-associated gene . The whole-genome sequence virulence analysis revealed a biofilm formation system and cell-cell adhesion-associated genes: , , , , , , , , , , , , and ; and quorum sensing-associated genes: and and iron acquisition system associated genes: , , , , , , , , , , , , , , , , , and . A sequence type classification based on the Pasteur scheme revealed that the isolate belongs to sequence type ST2. The mosaic of the virulence factors coupled with the resistance-associated genes and the phenotypic resistance profile highlights the risk that this strain is at this South African tertiary health facility.