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Updated: Jul 11, 2025
Experimental Human Pneumococcal Carriage
Published on: February 15, 2013
Value of pneumococcal PCR in respiratory samples for exclusion of pneumococcal pneumonia
Sam Van Goethem1,2, Philippe Van Lint3, Philippe Willems3
1Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium.
Background:
Streptococcus pneumoniae is the main aetiological agent in bacterial pneumonia. Therefore pneumococcal PCR is often included in respiratory multiplex PCR panels, both commercial and in-house. But respiratory PCR results for S. pneumoniae are difficult to interpret due to frequent non-pathogenic colonization on the mucosal surface of the upper airways with pneumococci or to cross-reaction of the PCR target in non-pneumococcal streptococci. In this study we investigated the value of lytA gene pneumococcal PCR in patients presenting with pneumonia.
Objectives:
To assess the utility of lytA gene detection for S. pneumoniae in a respiratory multiplex quantitative PCR (qPCR) panel for patients presenting with pneumonia.
Methods:
A retrospective study was conducted for lytA gene results as target for S. pneumoniae in hospitalized patients who were diagnosed with pneumonia and for which a respiratory multiplex PCR panel was performed. Patients were classified as 'probable', 'possible' or 'unlikely' of having a pneumococcal pneumonia.
Results:
A sensitivity of 71.4% and specificity of 89.6% were found, corresponding to a negative predictive value and positive predictive value of 97.6% and 34.2%, respectively, when considering 'probable' versus 'possible/unlikely'. In the PCR-positive cases we found a statistically significant difference in semi-quantitative Ct values between the 'probable' and the 'possible/unlikely' groups.
Conclusions:
We conclude that a negative qPCR for the lytA gene in a respiratory sample is highly predictive of a negative S. pneumoniae culture and is possibly sufficient to exclude S. pneumoniae as a causative agent. Respiratory pneumococcal PCR has a high negative predictive value for pneumococcal disease but the positive predictive value is low.
Insights
Pneumococcal PCR using the lytA gene is useful for diagnosing pneumonia. A negative test strongly suggests no pneumococcal infection, but a positive result requires further investigation due to potential non-pathogenic colonization.
Area of Science:
- Clinical Microbiology
- Infectious Diseases
- Respiratory Medicine
Background:
- Streptococcus pneumoniae is a primary cause of bacterial pneumonia.
- Pneumococcal PCR is common in respiratory panels but interpretation is challenging due to colonization and cross-reactivity.
- The lytA gene is a specific target for S. pneumoniae detection.
Purpose of the Study:
- To evaluate the utility of lytA gene detection in a respiratory multiplex quantitative PCR (qPCR) panel for diagnosing S. pneumoniae pneumonia.
- To assess the diagnostic accuracy of lytA qPCR in hospitalized pneumonia patients.
Main Methods:
- Retrospective analysis of lytA gene results from respiratory multiplex PCR panels in pneumonia patients.
- Classification of patients into 'probable', 'possible', or 'unlikely' pneumococcal pneumonia groups.
- Evaluation of sensitivity, specificity, and predictive values of the lytA PCR test.
Main Results:
- The lytA qPCR demonstrated a sensitivity of 71.4% and specificity of 89.6%.
- Negative predictive value was high at 97.6%, while positive predictive value was low at 34.2%.
- Significant differences in semi-quantitative Ct values were observed between 'probable' and 'possible/unlikely' pneumococcal pneumonia groups.
Conclusions:
- A negative lytA qPCR result in respiratory samples is highly predictive of the absence of S. pneumoniae.
- The lytA qPCR test shows a high negative predictive value for pneumococcal pneumonia, aiding in excluding the pathogen.
- The positive predictive value is limited, necessitating careful interpretation in clinical practice.
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