Characterization of Staphylococcus aureus Small-Colony Variants Isolated from Lower Respiratory Tract Specimens

Epidemiological data on small colony variants (SCVs) of Staphylococcus aureus (S. aureus) in China are lacking. This study aimed to investigate the prevalence and characteristics of S. aureus SCVs in patients with Pseudomonas aeruginosa (P. aeruginosa) pneumonia.

From October 2024 to September 2025, S. aureus SCVs were collected from lower respiratory tract specimens at two tertiary hospitals in Fuzhou and identified using MALDI-TOF MS. Antibiotic susceptibility testing was performed using a VITEK ^® 2 Compact System. Genetic diversity and virulence were analyzed using multilocus sequence typing (MLST), staphylococcal protein A (spa) typing, and toxin gene profiling. Biofilm formation was assessed using a microtiter plate assay, and patient characteristics were analyzed using the Hospital Information System.

Thirty-eight S. aureus SCVs (2.1%) were isolated from 1,832 lower respiratory tract specimens collected from patients with P. aeruginosa pneumonia. Compared to normal phenotype strains, SCVs exhibited smaller colonies and reduced hemolysis. Among resistant strains, 20 were methicillin-resistant S. aureus SCVs (MRSA-SCVs), with ST1-t128 (25.0%) being the most prevalent. ST764-t1084 MRSA-SCVs were resistant to penicillin, oxacillin, gentamicin, ciprofloxacin, levofloxacin, moxifloxacin, erythromycin, clindamycin, and tetracycline. Eighteen strains were methicillin-susceptible S. aureus SCVs (MSSA-SCVs), predominantly ST72-t3735 (16.7%). Virulence analysis showed adhesion-related gene carriage rates of 47.4-100.0% and immune evasion gene carriage rates of 52.6-73.7%. In addition, most S. aureus SCVs showed strong biofilm production.

This study identified a 2.1% prevalence of S. aureus SCVs (often undetected) in P. aeruginosa pneumonia patients. More than half of patients were methicillin-resistant (MRSA), with strong biofilm-forming capacity and a potential association with prolonged hospitalization. Vigilance is warranted against potential outbreaks of the predominant MRSA-SCV clone ST1-t128, as well as the severe drug resistance observed in ST764-t1084 MRSA-SCVs.