Genetic Diversity and Hospital Circulation of Opportunistic Pathogens in COVID-19 ICUs: Whole-Genome Sequencing Data

The COVID-19 pandemic led to a dramatic increase in healthcare-associated infections and antimicrobial resistance, particularly in intensive care units (ICUs). The aim of this study was to provide a comprehensive genomic characterisation of all clinically significant opportunistic pathogens (OPs) isolated from patients and the hospital environment in COVID-19 ICUs, and to use these data to reconstruct transmission pathways, identify reservoirs, and assess the molecular mechanisms of antimicrobial resistance and virulence. Whole-genome sequencing (WGS) was performed on 175 isolates isolated from patients and the hospital environment (including personal protective equipment, PPE) between 2021 and 2023. The species collection included nine OP species. Bioinformatic analysis included multilocus sequence typing, core genome single-nucleotide polymorphism analysis, phylogenetic reconstruction, and in silico detection of resistance and virulence genes and plasmid replicons. High-risk multidrug-resistant (MDR) clones were identified among Klebsiella pneumoniae, Acinetobacter baumannii, Escherichia coli, and Staphylococcus aureus. Core genome SNP analysis confirmed direct transmission of K. pneumoniae between patients and healthcare worker medical gloves. PPE was identified as a major reservoir, accounting for 68.4% of environmental isolates. The study demonstrates the power of WGS for high-resolution epidemiological surveillance, confirms the critical role of contaminated PPE in nosocomial transmission, and highlights the dominance of internationally spreading MDR clones in COVID-19 ICUs.