Diagnostic accuracy and clinical impact of respiratory specimen collection and microbiological testing strategies in patients with lower respiratory tract infections: a systematic review

Background: Respiratory specimen quality influences pathogen identification in lower respiratory tract infections. Microbiological testing also influences antibiotic decisions. This review examined diagnostic performance and clinical outcomes associated with collection methods, conventional microbiology, and rapid molecular testing. Methods: Eleven original study reports published before June 2026 were assembled for a structured narrative synthesis. Sampling strategies, diagnostic yield, agreement with culture, reporting time, antibiotic prescribing, and patient outcomes were examined separately. Clinical trials were distinguished from laboratory evaluations and retrospective estimates of prescribing changes. Results: Bronchoscopic sampling produced inconsistent clinical benefits compared with endotracheal aspiration. In community-acquired pneumonia, comprehensive molecular testing detected pathogens in 87% of patients versus 39% with culture-based methods. Molecular panels detected most culture-positive targets, alongside additional detections of uncertain clinical significance. Randomized trials demonstrated faster reporting and increased pathogen-directed treatment. One trial reduced inappropriate antibiotic exposure by 38.6 hours, while another increased results-directed treatment from 29% to 80%. Effects on overall antibiotic exposure, hospital stay, and mortality were inconsistent. In INHALE, antibiotic appropriateness improved, while non-inferiority for clinical cure was not established. Conclusions: Rapid molecular testing improves diagnostic yield and accelerates treatment targeting. Clinical benefit depends on specimen quality, interpretation of additional detections, and the prescribing response.