Clinical and Molecular Characterization of Viral-Bacterial Co-Infections in Upper Respiratory Tract Infections: Pathogen Profiles and Antimicrobial Resistance Patterns

Abstract

Background: Upper respiratory tract infections are among the prevalent infections at the present time, owing to the multiple viral and bacterial pathogens targeting the upper respiratory system. These infections can only be detected through the use of advanced diagnostic techniques, such as RT-PCR systems, which enable the identification of the most prominent viruses involved in upper respiratory tract infections, including Coronavirus, Influenza, Parainfluenza, RSV, and Adenovirus. . Bacterial isolates (Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Moraxella catarrhalis) were identified via standard microbiological procedures and API biochemical systems. Antimicrobial susceptibility testing (AST) was performed using the Kirby-Bauer disk diffusion method according to CLSI guidelines.
Results: the 500 samples, single viral infections were detected in 38.4% (n=192), single bacterial infections in 22.0% (n=110), and viral-bacterial co-infections in 28.4% (n=142). The most frequent co-infection profile involved Influenza A combined with Streptococcus pneumoniae (31.0%), followed by RSV with Staphylococcus aureus (22.5%). Patients with co-infections exhibited significantly higher clinical severity scores compared to those with viral mono-infections ( p < 0.001 ). Furthermore, bacterial strains isolated from co-infected cases demonstrated a strikingly higher rate of multidrug resistance (MDR) compared to mono-bacterial isolates (64.8% vs. 41.8%, p = 0.002