dRecent 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. Nonviable isolates and culture-negative clinical specimens were tested for the lytA gene and, if positive, were serotyped, using real-time PCRs. Multinomial regression analysis was used to determine the maximum lytA cycle threshold (C T ) value useful for predicting the ability to detect a serotype for the sample. The 2 test was used to compare the prevalence of serotypes between viable/nonviable isolates and culture-negative clinical specimens. Of 11,224 IPD cases reported, 1,091 (10%) were culture-negative samples and 981 (90%) of these were lytA positive. Samples with a lytA C T value of >35 were significantly less likely to be serotyped. A serotype/group was determined for 87% (737/844) of samples with a lytA C T value of <35, of which 60% (443/737) were identified as individual serotypes. The 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.
Streptococcus pneumoniae is a commensal bacterium of the upper respiratory tract, as well as a significant human pathogen. Each year, pneumococcal diseases result in Ͼ1 million deaths globally in children Ͻ5 years of age (1). The high burden of pneumococcal disease is also observed in elderly individuals, causing substantial morbidity and mortality (2). The polysaccharide capsule of the pneumococcus is an important virulence determinant (3, 4) and is the target for a number of pneumococcal vaccine formulations. At least 94 serotypes have been identified (5); however, only approximately 15 to 20 serotypes are responsible for the majority of disease worldwide (6).Culture remains the gold standard for diagnosis of pneumococcal disease due to its high specificity, but it has a low sensitivity and requires long incubation periods. Antibiotic therapy prior to specimen collection and suboptimal culturing conditions hinder the yield of cultures (7,8). PCR-based methods targeting pneumococcus-specific genes, such as lytA, have resulted in improved and timely diagnosis of pneumococcal disease (9-11).Determination of a pneumococcal serotype is important for surveillance and determining the effectiveness of polysaccharide-based vaccines. For decades, the Quellung reaction (12) has been the gold standard for serotyping; however, the method is culture dependent and therefore is not useful for culture-negative lytA-positive specimens. Sequencing of the capsular polysaccharide synthesis genes (13,14) has enabled the development of conventional (15) and real-time PCR (16-18) assays. The increased sensitivity of real-time PCR a...