Genetic characteristics of Staphylococcus aureus strains isolated from an intensive care unit of an infectious diseases hospital during the COVID-19 pandemic | CMAC

Genetic characteristics of Staphylococcus aureus strains isolated from an intensive care unit of an infectious diseases hospital during the COVID-19 pandemic

Clinical Microbiology and Antimicrobial Chemotherapy. 2025; 27(4):524-536

​ Smirnova S.S., Avdyunin D.D., Holmanskikh M.V., Stagilskaya Yu.S., Zhuykov N.N., Itani T.M
10.36488/cmac.2025.4.524-536
Staphylococcus aureus sequencing phylogenetic analysis molecular genetic analysis
Section
Personal Experience
Type
Original Article
Publication
Clinical Microbiology and Antimicrobial Chemotherapy. 2025; 27(4):524-536

Objective.

To provide a genetic characterization based on whole-genome sequencing (WGS) data of S. aureus isolates identified in one intensive care unit (ICU) during the COVID-19 pandemic.

Materials and Methods.

WGS on Illumina MiSeq was performed, generating twenty S. aureus sequences isolated from patients and environmental surfaces. Bioinformatic analysis included typing, identification of antimicrobial resistance (AMR) determinants, virulence factors, plasmid replicons, and phylogenetic analysis.

Results.

Significant genetic diversity was revealed, comprising four clonal complexes (CCs): CC15 – 6⁄20 (30%), CC8 – 3⁄20 (15%), CC22 – 2⁄20 (10%), and CC97 – 2⁄20 (10%); while 7⁄20 (35%) of isolates had an indeterminate CC. CC8 and CC22 isolates were detected exclusively on healthcare workers’ personal protective equipment (PPE). Phylogenetic analysis showed clustering with strains from diverse geographical regions. AMR genes conferring resistance to 9 antibiotic classes were identified, including β-lactams (blaZ, mecA), tetracyclines (tet(38)), and fosfomycine (fosB). Virulence genes (encoding immunesuppressing toxins, exoenzymes) were highly prevalent (> 90%). Plasmid replicons (e.g., rep16, rep5a) were identified in 17⁄20 (85%) of the isolates, indicating potential horizontal gene transfer of AMR determinants.

Conclusions.

These data demonstrate a complex S. aureus ecosystem within the ICU, characterized by high genetic diversity, a high prevalence of AMR and virulence determinants, and a significant plasmid pool. The predominance of isolates from PPE underscores the need for enhanced infection control measures to prevent the spread of potentially pathogenic and multidrug-resistant S. aureus strains in the hospital setting.

Svetlana S. Smirnova

Federal Research Institute of Viral Infections «Virome», Yekaterinburg, Russia

Avdyunin D.D.

Federal Research Institute of Viral Infections «Virome», Yekaterinburg, Russia

Holmanskikh M.V.

City Infectious Hospital, Nizhny Tagil, Russia

Stagilskaya Yu.S.

Federal Research Institute of Viral Infections «Virome», Yekaterinburg, Russia

Zhuykov N.N.

Federal Research Institute of Viral Infections «Virome», Yekaterinburg, Russia

Itani T.M

Federal Research Institute of Viral Infections «Virome», Yekaterinburg, Russia

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