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 pneumococca l carriage status. We tested this by comparing swab culture to quantitative culture and quantitative PCR of mucosal tissue in a rat model of pneumococ cal carriage. Quantitative culture and quantitative PCR identified signific antly 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 s pecificity of swab culture was 75/92% and 63/100% compared to quantitative tissue culture and quantitative PCR, respectively. The quantitative estimat es 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 quantita tive culture and PCR increases the number of positive samples by about one third.