Whole-genome sequencing identifies persistent transmission of a high-risk ST2 Acinetobacter baumannii clone in a...

Acinetobacter baumannii (A. baumannii) has posed a serious threat to the global healthcare environment due to its widespread multidrug resistance. However, the long-term molecular epidemiological characteristics, drug resistance profiles and genomic characteristics of A. baumannii isolates in Guangzhou, China have not been fully elucidated. This study aims to systematically analyze these characteristics using Acinetobacter baumannii strains from a local tertiary hospital.

A total of 98 non-repeating clinical isolates of A. baumannii collected between 2013 and 2021 were analyzed in the study. Whole genome sequencing technology (Illumina NovaSeq 6,000 platform) was also used for multi-locus sequence typing (MLST), resistance genomic/virulence genomic analysis (based on the CARD/VFDB database), plasmid screening (with the PlasmidFinder tool), and pan-genomic analysis (via the Roary tool).

Among the 21 identified STs, ST2 was the dominant lineage, accounting for 66.3% (65/98) of all isolates, indicating the establishment of a predominant epidemic clone. Compared with non-ST2 strains, ST2 isolates exhibited a significantly higher rate of carbapenem resistance (95.38%) and carried a higher burden of resistance determinants, including bla _OXA-23, bla _ADC-25, tet(B), and multiple aminoglycoside resistance genes. Notably, ST2 strains harbored a highly conserved and dominant repertoire of virulence factors, particularly those involved in iron acquisition and host adaptation, such as ompA, abaI, and the complete siderophore synthesis and uptake systems (basA-basJ, bauA-bauF, and entE). These features likely confer enhanced survival, persistence, and transmissibility in the hospital environment, supporting the classification of ST2 as a high-risk epidemic clone. Consistent with this, genomic clustering and temporal aggregation of ST2 isolates suggested sustained intrahospital transmission during the study period. Pangenome analysis revealed that A. baumannii possesses a large accessory genome (76.4%), reflecting substantial genomic plasticity that may facilitate rapid adaptation to antimicrobial and host-derived selective pressures.

As the first long-term genomic epidemiological study of A. baumannii in Guangzhou, our findings confirm that ST2 is the predominant multidrug-resistant and outbreak-prone lineage, driven by the convergence of resistance gene accumulation, virulence optimization, and genomic flexibility. These results underscore the urgent need to strengthen infection control measures and antimicrobial stewardship to curb the continued spread of this high-risk clone.