Isolation of pneumococcal DNA from nasopharyngeal samples for real-time, quantitative PCR: comparison of three methods.

BACKGROUND: Real-time PCR is a useful method for detecting and quantifying bacterial DNA in clinical samples. DNA extraction is a crucial step when performing quantitative PCR. METHODS: We compared three methods, QIAamp. The use of tradenames is for product identification purposes only and does not imply endorsement. DNA Mini kit, MagNAPure trade mark LC DNA Isolation Kit II together with PickPen trade mark magnetic particle transfer device, and KingFisher genomic DNA purification Kit with KingFisher mL instrument, for purification of Streptococcus pneumoniae DNA from 50 nasopharyngeal swab samples, collected into skim milk-tryptone-glucose-glycerin medium. Pneumococcal DNA was detected and quantified by real-time PCR and results were compared to culture findings. RESULTS: The 22 (44%) pneumococcal culture-positive specimens were all positive by PCR regardless of DNA extraction method used, except that one KingFisher-extracted sample was positive only when repeatedly tested. Additionally, 71%, 57%, and 82% of the culture-negative samples were positive by real-time PCR when DNA was extracted by QIAamp, MagNAPure-PickPen, and KingFisher methods, respectively. The number of genome equivalents detected by real-time PCR varied, but was mainly low in culture-negative samples. The sensitivities of culture and real-time PCR were hence compared by analyzing different dilutions of a pneumococcal suspension. Real-time PCR detected significantly higher numbers of genome equivalents than the numbers of bacteria detected by culture. CONCLUSIONS: The results indicate that the DNA extraction method used for quantitative PCR should be evaluated and that real-time PCR is more sensitive than bacterial culture for detecting pneumococcus in nasopharyngeal swab samples.

Diagnosis of Streptococcus pneumoniae and Haemophilus influenzae type b meningitis by identifying DNA from cerebrospinal fluid-impregnated filter paper strips.

BACKGROUND: Bacterial meningitis remains often etiologically unconfirmed, especially in resource-poor settings. We tested the potential of real-time polymerase chain reaction to identify Streptococcus pneumoniae (Pnc) and Haemophilus influenzae type b (Hib) from cerebrospinal fluid impregnated on filter paper strips. METHODS: Pnc and Hib genome equivalents were blindly quantified by polymerase chain reaction from 129 liquid cerebrospinal fluid (CSF) samples-the standard-and strips stored at room temperature for months. Genome counts were compared by simple regression. RESULTS: The strips showed a sensitivity and specificity of 92% and 99% for Pnc, and of 70% and 100% for Hib, respectively. The positive and negative predictive values were 94% and 97% for Pnc, and 100% and 89% for Hib, respectively. For Pnc, the positive and negative likelihood ratio was 92 and 0.08, and the overall accuracy 98%, whereas for Hib they were 70 and 0.30, and 91%, respectively. Genome counting showed good correlation between the filter paper and liquid CSF samples, r(2) being 0.87 for Pnc and 0.68 for Hib (P < 0.0001 for both). CONCLUSION: Although not replacing bacterial culture, filter paper strips offer an easy way to collect and store CSF samples for later bacteriology. They can also be transported in standard envelops by regular mail.

Does the presence of pneumococcal DNA in middle-ear fluid indicate pneumococcal etiology in acute otitis media?

Bacterial culture of middle-ear fluid (MEF), the standard for etiologic diagnosis of acute otitis media (AOM), has revealed Streptococcus pneumoniae (Pnc) to be a major pathogen responsible for one-third of AOM cases. In the present study, we compared the results of polymerase chain reaction (PCR) based on the amplification of the pneumolysin gene with the results of pneumococcal culture, for 2595 MEF samples obtained during AOM events in 831 children who were followed from 2-24 months of age in the Finnish Otitis Media Vaccine Trial. PCR results were positive for 47.1% of the MEF samples, and culture results were positive for 27.3% of the samples. PCR-positive, culture-negative samples were associated with previous Pnc AOM in a time-dependent pattern, concurrent antibiotic treatment, low volume of MEF, and concurrent nasopharyngeal carriage. PCR-positive AOM represented a clinically less severe disease, compared with culture-positive Pnc AOM. A positive PCR result seemed to indicate the presence of viable, although often nonculturable, Pnc.