Evaluating the feasibility, sensitivity, and specificity of next-generation molecular methods for pleural infection diagnosis
Authors: Bell Peter T. , Baird Timothy , Goddard John , Olagoke Olusola S. , Burke Andrew , Subedi Shradha , Davey Tiana R. , Anderson James , Sarovich Derek S. , Price Erin P. 
Published: October 2023

Rationale

Pleural infections are common and associated with substantial healthcare cost, morbidity, and mortality. Accurate pleural infection diagnosis remains challenging due to low culture positivity rates, frequent polymicrobial involvement, and non-specific diagnostic biomarkers.

Objective

To undertake a prospective pilot study examining the feasibility and challenges associated with molecular methods for diagnosing suspected pleural infection.

Methods

We prospectively characterised 26 consecutive, clinically suspected pleural infections, and 10 consecutive control patients with suspected non-infective pleural effusions, using shotgun metagenomics, bacterial metataxonomics, quantitative PCR, and conventional culture.

Results

We demonstrate the feasibility of culture-independent molecular techniques for diagnosing suspected pleural infection. Molecular methods exhibited excellent diagnostic performance, with each method identifying 54% (14/26) positive cases among the pleural infection cohort, versus 38% (10/26) with culture. Meta-omics methods unveiled complex polymicrobial infections largely missed by culture. Dominant infecting microbes included streptococci (S. intermedius,S. pyogenes,S. mitis),Prevotellaspp. (P. oris,P. pleuritidis), staphylococci (S. aureus,S. saprophyticus), andKlebsiella pneumoniae.However, we encountered challenges that complicated pleural infection interpretation, including: i) uncertainties regarding microbial pathogenicity and the impact of prior antibiotic therapy on diagnostic performance; ii) lack of a clinical diagnostic gold-standard for molecular performance comparisons; iii) potential accidental microbial contamination during specimen collection and processing; and iv) difficulties distinguishing background microbial noise from true microbial signal, particularly in low-biomass specimens.

Conclusions

Our pilot study demonstrates the potential utility and value of molecular methods in diagnosing pleural infection and highlights key concepts and challenges that should be addressed when designing larger prospective trials.

Key messages

What is already known on this topic

Confident pleural infection diagnosis is often challenging due to low culture positivity rates, frequent polymicrobial involvement, and non-specific diagnostic biomarkers. Limitations of conventional diagnostic tests result in prolonged and inappropriately broad-spectrum antimicrobial use, leading to potentially poorer patient outcomes and avoidable adverse effects.

What this study adds

We demonstrate the feasibility, utility, and challenges associated with the use of culture-independent molecular techniques for more accurate pleural infection diagnosis in a real-world clinical setting.

How this study might affect research, practice, or policy

These data will help to inform the design of larger prospective clinical trials and identify potential obstacles to be overcome as next-generation sequencing technologies become integrated into routine clinical practice.