Comparison of nasal swab culture, quantitative culture of nasal mucosal tissue and PCR in detecting Streptococcus pneumoniae carriage in rats

It is not known how well nasopharyngeal swab culture represents pneumococcal carriage status. We tested this by comparing swab culture to quantitative culture and quantitative PCR of mucosal tissue in a rat model of pneumococcal carriage. Quantitative culture and quantitative PCR identified significantly more carriers compared to swab culture (differences 15% and 33%, 95% CI 1-28% and 16-47%, p=0.04 and 0.001, respectively). The sensitivity and specificity of swab culture was 75/92% and 63/100% compared to quantitative tissue culture and quantitative PCR, respectively. The quantitative estimates of culture and PCR were very similar (Pearson correlation coefficient 0.79, p<0.001). In conclusion, even a well-controlled swab sampling markedly underestimates pneumococcal carriage rate, and simultaneous use of quantitative culture and PCR increases the number of positive samples by about one third.