Etiological characterization of acute respiratory tract infections and associated co-infections using Biofire...

Following the relaxation of non-pharmaceutical interventions post-COVID-19 pandemic, acute respiratory tract infections (ARTIs) have posed a substantial burden on healthcare settings, necessitating the implementation of rapid molecular diagnostic tools to improve pathogen identification and ensure early clinical management.

We conducted a retrospective study over one year (April 2024-March 2025) on 258 patients with ARTIs, admitted to a tertiary care hospital located in Egypt, to characterize their microbiological profile by Biofire respiratory 2.1 plus panel (RP 2.1). The demographic data and co-morbidities were systematically collected and analyzed from electronic medical records.

Of 160 patients testing positive for at least one respiratory pathogen by RP2.1 plus, 147 (91.8%) were positive for viral pathogens, 8(5%) for mixed viral-bacterial detections, and 5(3.2%) for bacterial detections. Detection of a single respiratory pathogen was observed among 71.8% of cases, with a statistically significant difference during autumn (27%, p = 0.03), and co-detections with multiple pathogens were observed among 28.2% of patients. Human rhinovirus (HRV) was the most common detected virus (52.5%), followed by Parainfluenza virus 1-4 (PIV,16.9%), seasonal Coronavirus species (15.6%), severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), and Influenza virus (INF) with equal frequency 10% each. Of 84 patients with HRV, 54 (64%) were infected with HRV only, and 30 (36%) had HRV co-detection. Patients with HRV co-detection were significantly more likely to be diagnosed with pneumonia than patients with HRV mono-detection (71.4% vs. 28.6%, p < 0.0001). Children in the age group less than 4 years old were more likely to be diagnosed with HRV co-detection than children with HRV only (60% versus 40% at p = 0.00). The most frequently detected respiratory pathogens with HRV were human coronavirus OC43 (4, 13.3%), followed by INFA (3,10%) and Mycoplasma pneumoniae (3,10%).

The current surge of respiratory pathogens post-COVID-19 pandemic calls for continuous monitoring of seasonal as well as co-detection patterns to mitigate potential health care burden and guide targeted public health interventions.

Not applicable.