Age and seasonal patterns of respiratory pathogens and their codetections revealed by multiplex PCR

Respiratory tract infections (RTIs) remain a major cause of morbidity worldwide owing to their diverse etiologies and overlapping clinical presentations. Multiplex real-time polymerase chain reaction (RT-qPCR) enables simultaneous detection of multiple respiratory pathogens and provides comprehensive epidemiological data. Following the COVID-19 pandemic, alterations in respiratory pathogen circulation and increasing recognition of viral–bacterial co-detection have highlighted the need for updated molecular epidemiological surveillance. This retrospective cross-sectional study included consecutive nasopharyngeal swab specimens obtained from patients with clinically suspected RTIs who underwent multiplex RT-qPCR testing at Siirt Training and Research Hospital, Türkiye, between January 2024 and December 2025. Patients were stratified into predefined age groups. Positive specimens were classified into mutually exclusive viral-only, bacterial-only, and viral–bacterial co-detection categories. Multivariable logistic regression analysis was performed to identify independent factors associated with respiratory pathogen detection. Among 1,666 nasopharyngeal swab specimens, respiratory pathogens were detected in 1,166 (70.0%). Bacterial-only detection accounted for 473 (40.6%), viral-only detection for 395 (33.9%), and viral–bacterial co-detection for 298 (25.6%) of positive specimens. Streptococcus pneumoniae and Haemophilus influenzae were the most frequently detected bacterial pathogens, whereas human rhinovirus and influenza A virus predominated among viral pathogens. Children had significantly higher odds of respiratory pathogen detection than adults (aOR 2.27, 95% CI 1.72–2.99; p < 0.001). Respiratory pathogen detection also varied significantly by season, with significantly lower odds during summer (aOR 0.58, 95% CI 0.43–0.78; p < 0.001) and autumn (aOR 0.57, 95% CI 0.43–0.75; p < 0.001) than during winter. Respiratory pathogen detection during the post-pandemic period demonstrated distinct age-related and seasonal patterns together with frequent viral–bacterial co-detection. Separate evaluation of viral-only, bacterial-only, and viral–bacterial co-detection provided a more comprehensive understanding of respiratory pathogen epidemiology. Because multiplex RT-qPCR detects microbial nucleic acids rather than confirming active infection, bacterial detections—particularly for common nasopharyngeal colonizers—should be interpreted together with clinical findings and complementary microbiological investigations.