Comparative genomic and resistance characterization of ST2 and ST164 carbapenem-resistant Acinetobacter baumannii from hospital environments and clinical specimens

Carbapenem-resistant Acinetobacter baumannii (CRAB) represents a formidable nosocomial pathogen, with healthcare environments acting as critical reservoirs for its dissemination. In this study, we investigated the prevalence, antimicrobial resistance profiles and genomic characteristics of CRAB isolates collected from hospitals in Shanghai, China, between June and December 2024, identifying ST2^Pas (84.13%) and ST164^Pas (15.08%) as the predominant lineages among the 126 CRAB isolates recovered from clinical (n=94), environmental (n=29) and healthcare worker (n=3) sources. Environmental CRAB accounted for the highest proportions on patient-contact surfaces (34.48%), medical devices (31.03%) and shared items (24.14%). Within the dominant ST2^Pas lineage, clinical isolates exhibited higher resistance rates to ampicillin/sulbactam, cefoperazone/sulbactam and levofloxacin, with significantly higher carriage rates of bla _TEM-1D compared to environmental isolates. Compared to ST164^Pas, ST2^Pas CRAB isolates exhibited greater resistance to amikacin, gentamicin, trimethoprim/sulfamethoxazole and minocycline and a higher prevalence of aph(3')-Ia, aph(3″)-Ib, aph(3')-VI, aph(6)-Id, armA, bla _OXA-66 , bla _TEM-1D, mph(E) and tet(B), but lower rates of bla _CARB-16, bla _NDM-1 and bla _OXA-91 (P<0.05). Notably, comparative genomic analysis suggested putative adaptive differences between the two lineages. ST2^Pas retained the T6SS and biofilm-associated genes (bap), descriptive genomic features that suggest a potential capacity for active colonization. Conversely, the ST164^Pas clone lacked the T6SS gene cluster but was enriched with the surface adhesin ata and immune evasion-related genes. Concordantly, ST164^Pas CRAB isolates exhibited significantly stronger biofilm-forming capacities than ST2^Pas in vitro. We hypothesize that these genomic alterations and phenotypic traits may represent a fitness trade-off, potentially conferring a survival advantage under antibiotic pressure. Furthermore, bla _OXA-23 in ST2^Pas was predominantly carried on conjugative plasmids restricted to Acinetobacter species, whereas bla _NDM-1 in ST164^Pas was localized on a broad-host-range non-mobile plasmid, potentially facilitating cross-genus transmission. Although our ST164^Pas isolates shared high homology with clinical strains from Zhejiang, China, the genomic localization of bla _NDM-1 differed between the plasmid and chromosome, respectively. These descriptive genomic findings highlight the putative adaptive trajectories of the predominant ST2^Pas and emerging ST164^Pas clones, underscoring the critical need for comprehensive genomic surveillance, complemented by future phenotypic validation, to monitor their rapid evolution and dissemination.