Environmental and Clinical Spread of MDR Acinetobacter baumannii: A Genomic Epidemiology Investigation

During the COVID-19 pandemic, healthcare systems experienced significant disruption, increasing the risk of multidrug-resistant (MDR) pathogen transmission. Acinetobacter baumannii, a critical-priority MDR pathogen, is known for its ability to persist in hospital environments and rapidly acquire resistance. To investigate the genomic characteristics, antimicrobial resistance determinants, and phylogenetic relationships of outbreak-associated Acinetobacter baumannii isolates, whole-genome sequencing (WGS) and comparative genomic analyses on 24 clinical and environmental strains collected during the COVID-19 period were performed. Twenty-four A. baumannii isolates collected between August 2020 and February 2021 from clinical and environmental samples were analyzed by WGS. All isolates displayed an MDR phenotype, with uniform resistance to carbapenems and aminoglycosides, and preserved colistin susceptibility. One environmental strain showed extreme drug resistance. WGS confirmed medium-quality genome assemblies and the clonal spread of a single A. baumannii lineage. Most resistance genes, including OXA-23, ADC-type β-lactamases, and ade efflux pumps, were chromosomally encoded and shared across all isolates. Plasmid-mediated resistance genes were variably distributed. This outbreak of MDR A. baumannii was driven by the clonal dissemination of a genomically stable lineage. Combined genomic and epidemiological analyses underscore the importance of integrated surveillance and environmental decontamination to prevent the spread of MDR pathogens.