Molecular Surveillance of Viral Genotypes and Aerobic Bacterial Coinfections in Respiratory Infections: Insights From a Tertiary Care Setting in Iran

Abstract

INTRODUCTION: Secondary bacterial infections play a pivotal role in the progression and outcomes of severe viral respiratory diseases. Comprehensive surveillance of both viral genotypes and bacterial pathogens is essential for guiding antimicrobial stewardship, reducing inappropriate antibiotic prescriptions, and preventing the rise of multidrug-resistant organisms. METHODS: Endotracheal aspirate (ETA) samples were collected from 150 patients admitted with viral respiratory infections, including SARS-CoV-2 cases. Bacterial isolates were identified through conventional and molecular techniques, and their antibiotic susceptibility profiles were determined according to Clinical and Laboratory Standards Institute (CLSI) guidelines. Viral genotyping was performed by sequencing the spike region. RESULTS: Among 150 patients, 135 (90) were confirmed as SARS-CoV-2 positive. Secondary bacterial respiratory infections were detected in 53 cases (39.2). Predominant isolates included Klebsiella pneumoniae (28.3, n = 15), Acinetobacter baumannii (18.9, n = 10), Escherichia coli (15.1, n = 8), Pseudomonas aeruginosa (9.4, n = 5), Staphylococcus aureus (9.4, n = 5), Shigella spp. (5.7, n = 3), Burkholderia spp. (3.8, n = 2), along with fungal infections (9.4, n = 5). High resistance rates were observed in A. baumannii and K. pneumoniae, whereas E. coli and S. aureus showed greater sensitivity. Viral sequencing identified Alpha (B.1.1.7, 30.2) and Delta (B.1.617.2, 69.8) variants among SARS-CoV-2 cases. DISCUSSION AND CONCLUSION: Findings highlight the importance of dual surveillance for viral genotypes and bacterial coinfections in respiratory diseases. Antimicrobial resistance among gram-negative pathogens poses a major clinical threat, underscoring the need for routine susceptibility testing. Integration of molecular virology with bacteriology not only improves patient outcomes during epidemics such as COVID-19, but also informs long-term strategies against emerging pathogens and resistant strains.