Metagenomic Study in Parapneumonic Effusion

Plain-language summary

Objective: To identify known and unknown bacterial pathogens in patients with pleural infections using a combination of conventional culture and next-generation sequencing approaches. Hypothesis to be tested: The investigators hypothesize that next-generation sequencing will serve as a comprehensive approach to identify culturable and unculturable bacterial pathogens in patients with pleural infections compared to the conventional culture. Design and subjects: This is a prospective cohort study to be conducted in the medical department of a tertiary care hospital in Hong Kong involving patients with pleural infection. Patients will be recruited if a pleural infection is suspected, with pleural fluid sampled and a 6-month follow-up. The clinical management by the medical team will not be interfered. Study instruments: Pleural fluid will be collected for conventional culture, 16S amplicon and shotgun metagenomic sequencing in parallel. The clinical information will be collected to clarify the causative correlation between symptoms, clinical outcomes and pathogen infections. Main outcome measures: The full spectrum of causative bacteria in pleural infection will be characterized. The diagnostic performance of identifying causative bacteria in pleural infection will be compared between the studied methods. The antimicrobial resistance pattern, clinical outcomes of pleural infection will also be compared between groups as categorized by the pattern of bacteriology identified by different methods. Data analysis: With reference to the conventional culture as the gold standard, sensitivity, specificity, positive predictive values and negative predictive values of 16S ribosomal ribonucleic acid (rRNA) gene amplicon and shotgun metagenomic sequencing will be calculated.

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