J Med Microbiol. 2015 Dec 1. doi: 10.1099/jmm.0.000204. [Epub ahead of print]

A novel quantitative PCR assay for the detection of Streptococcus pneumoniae using the competence regulator gene target comX.

Habets MN1, Cremers AJ2, Bos MP3, Savelkoul P4, Eleveld MJ5, Meis JF6, Hermans PW7, Melchers WJ8, de Jonge MI9,Diavatopoulos DA10.

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Abstract

Streptococcus pneumoniae is responsible for an estimated 1.6 million deaths worldwide every year. Whilst rapid detection and timely treatment with appropriate antibiotics is preferred, this is often difficult due to the amount of time that detection with blood cultures takes. In this study, a novel quantitative PCR assay for the detection of S. pneumoniae was developed. To identify novel targets, we analyzed the pneumococcal genome for unique, repetitive DNA sequences. This approach identified comX, which is conserved and present in duplicate copies in S. pneumoniae, but not in other bacterial species. Comparison to lytA, the current gold standard for detection by quantitative PCR, demonstrated an analytic specificity of 100 % for both assays on a panel of 10 pneumococcal and 18 non-pneumococcal isolates, but a reduction of 3.5 Cq values (+/- 0.23 SEM) resulting in an increased analytical detection rate of comX. We validated our assay on DNA extracted from serum of 30 bacteraemic patients that were blood culture positive for S. pneumoniae and 51 serum samples that were culture positive for other bacteria. This resulted in a similar clinical sensitivity between the comX and lytA assay (47 %) and in a diagnostic specificity of 98.2 % and 100 % for the lytA and the comX assay respectively. In conclusion, we have developed a novel quantitative PCR assay with increased analytical sensitivity for the detection of S. pneumoniae, which may be used to develop a rapid bedside test for the direct detection of S. pneumoniae in clinical specimens.

PMID: 26628261 [PubMed - as supplied by publisher]