Performance of next-generation molecular methods in the diagnosis of pleural space infections and their aetiology

Abstract

AbstractPleural space infections (PSIs) are common and associated with substantial healthcare cost, morbidity, and mortality. Accurate PSI diagnosis remains challenging due to low culture positivity rates, frequent polymicrobial involvement, and non-specific diagnostic biomarkers. To better understand the comparative diagnostic yield of culture-independent technologies for PSI diagnosis, we prospectively characterised 26 clinically suspected PSIs and 10 control patients with non-infective pleural effusions using shotgun metagenomics, bacterial metataxonomics, quantitative PCR, and conventional culture. We demonstrate that culture-independent molecular techniques have superior sensitivity and negative predictive values for PSI diagnosis compared with conventional culture. Bacterial metataxonomics and metagenomics were both sensitive to the detection of polymicrobial infections, and unveiled microbial heterogeneity. Metagenomics also detected fungi and DNA viruses within pleural fluid. Dominant pathogens in the PSI cohort according to the highest resolution method, metagenomics, included streptococci (S. intermedius,S. pyogenes,S. mitis),Prevotellaspp. (P. oris,P. pleuritidis), staphylococci (S. aureus,S. saprophyticus), andKlebsiella pneumoniae.Taken together, these results demonstrate the potential utility of molecular methods in the accurate diagnosis of PSI, which represents an important step towards improving personalised treatment decision-making and antimicrobial stewardship in suspected PSI.