Genetic Characteristics of Acinetobacter baumannii Isolates Circulating in an Intensive Care Unit of an Infectious Diseases Hospital During the COVID-19 Pandemic

During the COVID-19 pandemic, a significant increase in the spread of healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) was observed. Acinetobacter baumannii, particularly carbapenem-resistant strains, poses a serious threat in intensive care units (ICUs). This study aimed to genetically characterize A. baumannii isolates from the ICU of an infectious diseases hospital repurposed for COVID-19 patient treatment. Whole-genome sequencing (WGS) was performed on 56 A. baumannii isolates from patients and environmental surfaces using the Illumina MiSeq platform. Bioinformatic analysis included multi-locus sequence typing (MLST), core-genome MLST (cgMLST), phylogenetic analysis, and in silico detection of antimicrobial resistance genes. Three sequence types (STs) were identified: ST2 (35.7%), ST78 (30.4%), and ST19 (3.5%); while 30.4% of the isolates were non-typeable. Phylogenetic analysis revealed clustering of ST2 with isolates from East Africa, ST78 with European isolates, and ST19 with isolates from Germany and Spain. Resistance genes to eight classes of antimicrobials were detected. All isolates were resistant to aminoglycosides and β-lactams. The blaOXA-23 carbapenemase gene was present in all ST2 isolates. cgMLST analysis (cgST-1746) showed significant heterogeneity among ST2 isolates (24–583 allele differences), indicating microevolution within the hospital. A novel synonymous SNP (T2220G) in the rpoB gene was identified. Environmental sampling highlighted the role of contaminated personal protective equipment (PPE) in transmission, with 47.0% of ST2 and 64.3% of ST78 isolates found on PPE. The study underscores the high resolution of WGS and cgMLST for epidemiological surveillance and confirms the critical role of infection control measures in preventing the spread of multidrug-resistant A. baumannii.