Multiplex real-time pcr for detection of respiratory viruses in pediatric cystic fibrosis patients: viral-bacterial co-infection patterns and clinical associations in Tehran, Iran (2023–2024)

Cystic fibrosis (CF) patients are at increased risk for respiratory complications from viral infections. This study evaluated the prevalence of Influenza A/B, Respiratory Syncytial Virus (RSV), and SARS-CoV-2 in pediatric CF patients and characterized viral-bacterial co-infection patterns during the post-COVID-19 period in Tehran, Iran (2023–2024). A total of 113 respiratory samples were collected from pediatric CF patients (aged 2.5 months to 18 years). Viral RNA was extracted and analyzed using a multiplex TaqMan-based real-time PCR assay targeting SARS-CoV-2, Influenza A/B, and RSV. Bacterial/fungal co-infections were identified by standard microbiological culture. Viral pathogens were detected in 19 samples (16.81%); Influenza A/B was the only virus detected among the pathogens included in the multiplex PCR panel. All viral-positive cases occurred in patients experiencing pulmonary exacerbation (32.8%; p -value < 0.0001), with no significant associations with gender ( p -value = 0.322), age group ( p -value = 0.26), or season ( p -value = 0.50). Bacterial/fungal co-infection was detected in 89.47% of viral-positive cases, with Pseudomonas aeruginosa as the most common pathogen (47.4%). No bacterial or fungal genera showed significant association with influenza infection. Influenza A/B detection was significantly associated with pulmonary exacerbation episodes in this cohort. Although no significant association was observed between bacterial/fungal colonization with the phase of the disease, the importance of this matter cannot be overlooked. Routine multiplex PCR testing during exacerbation may improve disease management in this population.