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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
Published on: December 22, 2014
Metagenomic Analysis of Thoracic Empyema Etiology Through Next-Generation Sequencing Enhances Conventional Culture
Dewi Anggraini1,2,3, Indra Yovi2,4,5, Aisyah Elliyanti6
1Department of Microbiology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia.
Background:
This study aimed to analyze the microbiome of thoracic empyema using metagenomic methods and compare the results with conventional culture methods to increase diagnostic accuracy and enhance antibiotic therapy.
Materials And Methods:
This study involved 30 patients with thoracic empyema from hospitals in Riau Province, Indonesia. Pleural fluid samples were collected for culture analysis and identification using the Vitek 2 compact system and metagenomic analysis. Patient clinical data were also collected.
Results:
Culture methods showed a 40.0% positive rate, with Gram-negative bacteria (Klebsiella pneumoniae and Pseudomonas aeruginosa) predominating. Metagenomics showed a 56.7% positive rate, identifying a more diverse microbiome, including fungi (29.4% abundance), other Gram-negative bacteria (26.5%), and anaerobic bacteria (22.5%). Comparison of the two methods showed 36.7% complete agreement and 23.3% partial agreement, with 40% disagreement, with a Kappa coefficient of 0.416 and P-value of 0.016 (P<0.050).
Conclusion:
Metagenomic NGS offers significant advantages in detecting the microbiome of thoracic empyema, particularly fungi and anaerobic bacteria, which are often missed by conventional culture methods. This has the potential to improve diagnostic accuracy and optimize antibiotic therapy. Further research with larger sample sizes is needed.
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