J Clin Microbiol. 2014 Jun 23. pii: JCM.01061-14. [Epub ahead of print]
Challenges of using molecular serotyping for pneumococcal disease surveillance.
Recent advances in the molecular identification and serotyping of Streptococcus pneumoniae are useful for culture-negative samples; however, there are limitations associated with these methods. We aimed to assess the value of molecular assays for invasive pneumococcal disease (IPD) surveillance in South Africa from 2010 through 2012. Non-viable isolates and culture-negative clinical specimens were tested for the lytA gene, and if positive were serotyped, using real-time PCR. Multinomial regression analysis was used to determine the maximum lytA Ct-value useful for predicting the ability to detect a serotype for the sample. The χ2-test was used to compare the prevalence of serotypes between viable/non-viable isolates and culture-negative clinical specimens. Of 11,224 IPD cases reported, 1091 (10%) were culture-negative samples and 981 (90%) of these were lytA-positive. Samples with a lytA Ct-value ≥35 were significantly less likely to be serotyped. A serotype/group was determined for 87% (737/844) of samples with a lytA Ct-value <35, of which 60% (443/737) were identified as individual serotypes. Serotype prevalence did not differ significantly between isolates and culture-negative specimens. Although molecular serotyping added 7% (737/11,224) serotyping data, the inability to resolve 40% of samples to single serotypes remains a challenge for serotype-specific data analysis.
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