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COMPARISON OF CONVENTIONAL CULTURE AND REAL TIME PCR (RT-PCR) BASED DIRECT DETECTION METHOD FOR THE IDENTIFICATION OF PNEUMOCOCCAL COLONIZATION IN CHILDREN
Real time PCR (RT-PCR) is an alternative approach for the identification and quantification of pneumococci directly from samples.
To compare pneumococcal detection rates using culture and RT-PCR and to compare pneumococcal colonization density in healthy children and hospitalized children with respiratory symptoms.
284 nasopharyngeal swabs (NPSs) obtained from children between 2 months to 2 years of age were included; 101 were from healthy children while 183 were from children with respiratory symptoms. An RT-PCR assay targeting lytA was done alongside with culture based methods.
A standard curve was plotted using DNA from ATCC 49619 strain of Streptococcus pneumoniae with a 10-fold dilution series. RT-PCR positivity as defined by a Cq value of =< 35
The overall colonization rate detected by conventional culture was 41.2% (n=117) while RT-PCR detection rate was 43.7% (n=124). The colonization rate detected by RT-PCR in the healthy cohort was 33.7% (n=34) and it was 49.2% (n=90) in the hospitalized cohort. It was 37.6% (n=38) and 43.2% (n=79) for the two cohorts by culture. The mean Cq value for the healthy cohort was 29.61±2.85 and 28.93±3.62 for the hospitalized cohort.
The mean genomic DNA copy numbers detected in children with respiratory symptoms was log10 7.49 (SD 1.07) while it was log10 7.30 (SD 0.23) in healthy children.
There was a higher detection of pneumococcal colonization using RT-PCR.
A higher pneumococcal colonization density was detected in hospitalized children with respiratory symptoms.
Research grant WI216479 through Pfizer for financial assistance.