Multiplex PCR-Based Characterization of Respiratory Pathogen Detection, Co-Occurrence Patterns, and Culture Discordance in Hospitalized Adults with Community-Acquired Pneumonia (CAP)

Multiplex molecular testing has expanded respiratory pathogen detection, but contemporary data from the Gulf region remain limited. This retrospective observational study characterized respiratory pathogen detection and co-occurrence patterns and evaluated agreement between multiplex PCR and conventional respiratory culture among adults hospitalized with community-acquired pneumonia in Dubai, United Arab Emirates, between January 2022 and January 2025. Among 278 patients, at least one PCR target was detected in 232 (83.5%; 95% CI 78.6–87.4); 126 (45.3%; 95% CI 39.6–51.2) had single-organism detection, 106 (38.1%; 95% CI 32.6–44.0) had multiple-organism detection, and 46 (16.5%; 95% CI 12.6–21.4) had no target detected. The most frequently detected organisms were Haemophilus influenzae (29.5%), Streptococcus pneumoniae (25.2%), human rhinovirus (16.9%), Legionella pneumophila (15.8%), and influenza A virus (11.9%). Among 242 patients with respiratory culture available, shared bacterial targets were detected by both methods in 12 patients, by PCR alone in 156, by culture alone in two, and by neither method in 72. Positive percent agreement was 85.7%, negative percent agreement was 31.6%, overall agreement was 34.7%, and Cohen’s κ was 0.027. Multiplex PCR demonstrated a high molecular detection yield and revealed frequent, heterogeneous multiple-organism detection patterns. Molecular findings should be interpreted alongside clinical assessment and conventional culture.