Respiratory pathogen detection and Co-detection in hospitalized children with lower respiratory tract infections using multiplex RT-qPCR: A single-center retrospective Observational Study
Yunus Nas, Süveyda Gözüküçük, Bekir Sami Uyanık, Basri ÇakıroğluBackground
Lower respiratory tract infections (LRTIs) are a common cause of pediatric hospitalization, but distinguishing viral from bacterial etiologies based solely on clinical findings remains challenging. Multiplex real-time polymerase chain reaction (RT-qPCR) enables the simultaneous detection of multiple respiratory pathogen targets. However, molecular detection does not necessarily establish microbial causation, particularly for bacteria identified in upper respiratory tract specimens.
Objectives
To describe respiratory pathogen detection and co-detection patterns in hospitalized children with LRTIs using multiplex RT-qPCR.
Design
A single-center retrospective observational study.
Methods
We evaluated 242 hospitalized children with clinically diagnosed LRTIs who underwent multiplex respiratory RT-qPCR testing between October 2021 and April 2026 at a tertiary-care hospital in Istanbul, Türkiye. Nasopharyngeal swab specimens were analyzed for respiratory viral and bacterial targets. All listed targets, including SARS-CoV-2, were assessed in the total study population. Pathogen-specific detection frequencies and single- and multiple-pathogen detection patterns were evaluated. Molecular findings were additionally classified as viral-only, bacterial-only, viral–bacterial co-detection, or no pathogen detected.
Results
At least one respiratory pathogen target was detected in 190 of 242 children (78.5%). Among pathogen-positive children, single-pathogen detection occurred in 103 (54.2%) and multiple-pathogen detection in 87 (45.8%). Dual detection was the most frequent multiple-detection pattern (53/87; 60.9%), followed by triple (21/87; 24.1%), quadruple (10/87; 11.5%), quintuple (2/87; 2.3%), and sextuple detection (1/87; 1.1%). The most frequently detected targets were
Conclusion
Respiratory pathogen detection and co-detection were common among hospitalized children. Viral-only detection was the most frequent pattern. Because nasopharyngeal bacterial detections may reflect upper-airway colonization, these findings should be interpreted as descriptive detection patterns rather than definitive evidence of LRTI causation.