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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
Published on: December 22, 2014
The bacteriology of pleural infection (TORPIDS): an exploratory metagenomics analysis through next generation
Nikolaos I Kanellakis1, John M Wrightson2, Stephen Gerry3
1Oxford Centre for Respiratory Medicine, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Laboratory of Pleural and Lung Cancer Translational Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences, China Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
Background:
Pleural infection is a common and severe disease with high morbidity and mortality worldwide. The knowledge of pleural infection bacteriology remains incomplete, as pathogen detection methods based on culture have insufficient sensitivity and are biased to selected microbes. We designed a study with the aim to discover and investigate the total microbiome of pleural infection and assess the correlation between bacterial patterns and 1-year survival of patients.
Methods:
We assessed 243 pleural fluid samples from the PILOT study, a prospective observational study on pleural infection, with 16S rRNA next generation sequencing. 20 pleural fluid samples from patients with pleural effusion due to a non-infectious cause and ten PCR-grade water samples were used as controls. Downstream analysis was done with the DADA2 pipeline. We applied multivariate Cox regression analyses to investigate the association between bacterial patterns and 1-year survival of patients with pleural infection.
Findings:
Pleural infection was predominately polymicrobial (192 [79%] of 243 samples), with diverse bacterial frequencies observed in monomicrobial and polymicrobial disease and in both community-acquired and hospital-acquired infection. Mixed anaerobes and other Gram-negative bacteria predominated in community-acquired polymicrobial infection whereas Streptococcus pneumoniae prevailed in monomicrobial cases. The presence of anaerobes (hazard ratio 0·46, 95% CI 0·24-0·86, p=0·015) or bacteria of the Streptococcus anginosus group (0·43, 0·19-0·97, p=0·043) was associated with better patient survival, whereas the presence (5·80, 2·37-14·21, p<0·0001) or dominance (3·97, 1·20-13·08, p=0·024) of Staphylococcus aureus was linked with lower survival. Moreover, dominance of Enterobacteriaceae was associated with higher risk of death (2·26, 1·03-4·93, p=0·041).
Interpretation:
Pleural infection is a predominantly polymicrobial infection, explaining the requirement for broad spectrum antibiotic cover in most individuals. High mortality infection associated with S aureus and Enterobacteriaceae favours more aggressive, with a narrower spectrum, antibiotic strategies.
Funding:
UK Medical Research Council, National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust, Oxfordshire Health Services Research Committee, Chinese Academy of Medical Sciences, and John Fell Fund.
Insights
Pleural infection is often polymicrobial. The presence of anaerobes or Streptococcus anginosus group bacteria improves survival, while Staphylococcus aureus or Enterobacteriaceae dominance is linked to higher mortality.
Area of Science:
- Microbiology
- Infectious Diseases
- Genomics
Background:
- Pleural infection poses a significant global health burden with high morbidity and mortality.
- Current pathogen detection methods for pleural infection lack sensitivity and are biased.
- The complete microbiome of pleural infection and its impact on patient outcomes require further investigation.
Purpose of the Study:
- To comprehensively characterize the microbiome in pleural infection.
- To identify bacterial patterns associated with patient survival.
- To improve diagnostic and therapeutic strategies for pleural infections.
Main Methods:
- 16S rRNA next-generation sequencing was performed on 243 pleural fluid samples.
- Samples were obtained from a prospective observational study (PILOT study).
- Multivariate Cox regression analyses assessed the association between bacterial patterns and 1-year survival.
Main Results:
- Pleural infections were predominantly polymicrobial (79%).
- Anaerobes and Streptococcus anginosus group bacteria were associated with better 1-year survival.
- Staphylococcus aureus and Enterobacteriaceae dominance correlated with increased mortality risk.
Conclusions:
- Pleural infection is typically polymicrobial, necessitating broad-spectrum antibiotics.
- Specific bacterial profiles, such as S. aureus and Enterobacteriaceae, indicate a need for targeted, aggressive antibiotic strategies.
- Understanding the pleural infection microbiome can guide personalized treatment approaches.
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