Evaluating the feasibility, sensitivity, and specificity of next-generation molecular methods for pleural infection diagnosis

Peter T Bell; Timothy Baird; John Goddard; Olusola S Olagoke; Andrew Burke; Shradha Subedi; Tiana R Davey; James Anderson; Derek S Sarovich; Erin P Price

doi:10.1128/spectrum.01960-24

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Evaluating the feasibility, sensitivity, and specificity of next-generation molecular methods for pleural infection diagnosis

Journal article

Open access

Peer reviewed

Evaluating the feasibility, sensitivity, and specificity of next-generation molecular methods for pleural infection diagnosis

Peter T Bell, Timothy Baird, John Goddard, Olusola S Olagoke, Andrew Burke, Shradha Subedi, Tiana R Davey, James Anderson, Derek S Sarovich and Erin P Price

Microbiology Spectrum, Vol.13(2), e01960-24

2025

DOI: https://doi.org/10.1128/spectrum.01960-24

PMCID: PMC11792517

PMID: 39812555

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Abstract

empyema

metagenomics

high-throughput sequencing

parapneumonic effusion

pleural infection

microbiome

Pleural infections are common and associated with substantial healthcare costs, morbidity, and mortality. Accurate diagnosis remains challenging due to low culture positivity rates, frequent polymicrobial involvement, and non-specific diagnostic biomarkers. Here, we undertook a prospective study examining the feasibility and performance of molecular methods for diagnosing suspected pleural infection. We prospectively characterized 26 consecutive clinically suspected pleural infections, and 10 consecutive patients with suspected non-infective pleural effusions, using shotgun metagenomics, bacterial metataxonomics, quantitative PCR, and conventional culture. Molecular methods exhibited excellent diagnostic performance, with each method identifying 54% (14 out of 26) positive cases among the pleural infection cohort, versus 38% (10 out of 26) with culture. Metagenomics and bacterial metataxonomics unveiled complex polymicrobial infections that were not captured by culture. Dominant microbes included streptococci (Streptococcus intermedius, Streptococcus pyogenes, and Streptococcus mitis), Prevotella spp. (Prevotella oris and Prevotella pleuritidis), staphylococci (S. aureus and S. saprophyticus), and Klebsiella 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 microbial contamination during specimen collection or processing; and (iv) difficulties distinguishing background microbial noise from true microbial signal in low-biomass specimens. This 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.

Details

Title: Evaluating the feasibility, sensitivity, and specificity of next-generation molecular methods for pleural infection diagnosis
Authors: Peter T Bell - Sunshine Coast University Hospital
Timothy Baird - University of the Sunshine Coast, Queensland, Centre for Bioinnovation
John Goddard - Griffith University
Olusola S Olagoke - University of the Sunshine Coast, Queensland, Centre for Bioinnovation
Andrew Burke - The University of Queensland
Shradha Subedi - Sunshine Coast University Hospital
Tiana R Davey - University of the Sunshine Coast, Queensland, Centre for Bioinnovation
James Anderson - Sunshine Coast University Hospital
Derek S Sarovich - University of the Sunshine Coast, Queensland, Centre for Bioinnovation
Erin P Price (Corresponding Author) - University of the Sunshine Coast, Queensland, Centre for Bioinnovation
Publication details: Microbiology Spectrum, Vol.13(2), e01960-24
Publisher: American Society for Microbiology
Date published: 2025
DOI: 10.1128/spectrum.01960-24
ISSN: 2165-0497
PMID: 39812555; PMC11792517
Data Availability: Raw bacterial 16S rRNA metataxonomic sequencing reads are available at NCBI BioProject PRJNA972883. Human-depleted metagenomic reads are available at BioProject PRJNA972883. Assemblies are available via BioProject PRJNA970939.
Grant note: This work was funded by Wishlist Sunshine Coast Hospital Foundation (award 2021-04-CRG to T.B., O.S.O., J.G., D.S.S., and E.P.P.) and Advance Queensland (awards AQIRF0362018 to E.P.P. and AQIRF095-2020-CV to O.S.O.).
Organisation Unit: School of Health - Biomedicine; School of Science, Technology and Engineering; Centre for Bioinnovation; School of Health and Behavioural Sciences - Legacy
Language: English
Record Identifier: 991094092402621
Output Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Web Of Science research areas: Microbiology

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