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The development of a 16S rRNA gene based PCR for the identification of Streptococcus pneumoniae and comparison with four other species specific PCR assays

Nabil Abdullah El Aila1, Stefan Emler2, Tarja Kaijalainen3, Thierry De Baere14, Bart Saerens1, Elife Alkan1, Pieter Deschaght1, Rita Verhelst1 and Mario Vaneechoutte1*

Author Affiliations

1 Laboratory Bacteriology Research, Department of Chemistry, Microbiology and Immunology, University of Ghent, Ghent, Belgium

2 SmartGene, Zug, Switzerland

3 National Reference Laboratory for Pneumococcus, National Institute for Health and Welfare (THL), Oulu, Finland

4 Scientific Institute of Public Health, Brussels, Belgium

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BMC Infectious Diseases 2010, 10:104  doi:10.1186/1471-2334-10-104

Published: 29 April 2010



Streptococcus pneumoniae is one of the most frequently encountered pathogens in humans but its differentiation from closely related but less pathogenic streptococci remains a challenge.


This report describes a newly-developed PCR assay (Spne-PCR), amplifying a 217 bp product of the 16S rRNA gene of S. pneumoniae, and its performance compared to other genotypic and phenotypic tests.


The new PCR assay designed in this study, proved to be specific at 57°C for S. pneumoniae, not amplifying S. pseudopneumoniae or any other streptococcal strain or any strains from other upper airway pathogenic species. PCR assays (psaA, LytA, ply, spn9802-PCR) were previously described for the specific amplification of S. pneumoniae, but psaA-PCR was the only one found not to cross-react with S. pseudopneumoniae.


Spne-PCR, developed for this study, and psaA-PCR were the only two assays which did not mis-identify S. pseudopneumoniae as S. pneumoniae. Four other PCR assays and the AccuProbe assay were unable to distinguish between these species.