Tracking the Environmental and Clinical Spread of MDR Acinetobacter baumannii During COVID-19 Through Genomic Epidemiology

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, resistance determinants, and transmission dynamics of a nosocomial outbreak of A. baumannii at a tertiary care hospital in Northern Italy, twenty-four A. baumannii isolates collected between August 2020 and February 2021 from clinical and environmental samples were analyzed. Whole genome sequencing (WGS) was conducted. Genomes were reconstructed and analyzed for clonal relatedness, resistance genes, and phylogenetic profiles. All isolates displayed an MDR phenotype, with uniform resistance to carbapenems and aminoglycosides, and preserved colistin susceptibility. One environmental strain showed extensive drug resistance. WGS confirmed high-quality genome assemblies and clonal spread of a single A. baumannii lineage. Most resistance genes, including OXA-66, 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 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.