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Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
Empyema: the use of broad range 16S rDNA PCR for pathogen detection
S Saglani1, K A Harris, C Wallis
1Department of Respiratory Paediatrics, Great Ormond Street Hospital for Children, Great Ormond Street, London, UK.
Background:
An increase in the incidence of thoracic empyema in children has been reported. The causative pathogen is often unknown as pleural fluid is frequently sterile at the time of culture. The role of unusual organisms is unclear.
Aims:
(1) To compare the detection of organisms in pleural fluid from children with empyema using a molecular technique (16S rDNA polymerase chain reaction (PCR)) and bacterial culture. (2) To compare the concordance of organisms identified using the two techniques and the influence of prior antibiotic treatment on positive detection rate.
Methods:
Pleural fluid from children admitted with empyema between January 2000 and February 2002 was cultured and additionally analysed using broad range 16S rDNA PCR.
Results:
Pleural fluid was cultured from 32 patients, aged 1 month-16 years. Median duration of previous antibiotic therapy was 8 days (range 1-42 days). Six samples were culture positive and 22 were PCR positive. A causal organism was detected by PCR alone, after considering results from the local hospital, in 14 patients. There was complete concordance in organisms cultured and detected by PCR. Additional organisms detected by PCR were predominantly S pneumoniae, S pyogenes, and anaerobes.
Conclusions:
Analysis of pleural fluid by broad range 16S rDNA PCR in addition to culture, increases organism identification in empyema.
Insights
Broad-range 16S rDNA PCR significantly improves organism detection in pediatric empyema cases compared to bacterial culture alone. This molecular technique enhances identification of causative pathogens, even after antibiotic treatment.
Area of Science:
- Pediatric Infectious Diseases
- Microbiology
- Molecular Diagnostics
Background:
- Pediatric thoracic empyema incidence is rising.
- Causative pathogens are often unidentified due to sterile pleural fluid cultures.
- The role of uncommon microorganisms remains unclear.
Purpose of the Study:
- Compare 16S rDNA PCR with bacterial culture for organism detection in pediatric empyema.
- Assess concordance between PCR and culture.
- Evaluate antibiotic treatment's impact on detection rates.
Main Methods:
- Pleural fluid samples from pediatric empyema patients were analyzed.
- Samples underwent both bacterial culture and broad-range 16S rDNA PCR.
- Patient data included age and prior antibiotic therapy duration.
Main Results:
- PCR identified organisms in 22 of 32 samples, versus 6 for culture.
- 16S rDNA PCR alone identified a causal organism in 14 additional patients.
- Complete concordance was observed for organisms detected by both methods; PCR identified S pneumoniae, S pyogenes, and anaerobes more frequently.
Conclusions:
- Broad-range 16S rDNA PCR enhances organism identification in pediatric empyema.
- This molecular method is valuable alongside traditional culture techniques.
- Improved pathogen detection aids in understanding and managing pediatric empyema.
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