Abstract
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), Prevotella spp. (P. oris, P. pleuritidis), staphylococci (S. aureus, 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 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.
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.
Competing Interest Statement
The authors have declared no competing interest.
Funding Statement
This work was funded by Wishlist Sunshine Coast Hospital Foundation (award 2021-04-CRG to TB, OO, JG, DSS, and EPP) and Advance Queensland (awards AQIRF0362018 to EPP and AQIRF095-2020-CV to OSO).
Author Declarations
I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.
Yes
The details of the IRB/oversight body that provided approval or exemption for the research described are given below:
The study was approved by The Prince Charles Hospital Human Research Ethics Committee (HREC) HREC/2022/QPCH/81858 and the Sunshine Coast Hospital and Health Service Research Governance Office. All participants provided written informed consent.
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Yes
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Yes
Footnotes
Minor updates have been made to the manuscript to comply with the STARD checklist, as per the Equator Network guidelines.
Data Availability
All sequence data generated in this study are available via NCBI BioProject PRJNA972883; genome assemblies are available via NCBI BioProject PRJNA970939.