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National surveillance of invasive pneumococcal disease (IPD) includes serotypingStreptococcus pneumoniae(SP) isolates from sterile site cultures. PCR is more sensitive and can identify more SP serotypes (STs) in culture-negative samples. The aim of this study was to determine whether enhanced surveillance of childhood empyema, using PCR, provides additional serotype information compared with conventional surveillance.Pleural fluid (PF) from children with empyema were cultured and tested by PCR to identify SP, targeting the autolysin gene (lytA). Multiplex PCR-based reverse line blot assay was used to identify SP STs. Corresponding IPD surveillance and serotype data were obtained from the National Notifiable Diseases Surveillance System (NNDSS).Eighty-nine children with empyema, aged ≤16 years, were recruited between April 2008 and March 2009, inclusive. SP was isolated from 5/84 (5.9%) PF cultures and by PCR in 43/79 (54.4%) PF samples. Serotypes were unidentifiable in 15 samples. The frequency of six serotypes (or serotype pairs) identified in 28 samples, including one with two serotypes, were: ST1,n= 4/29 (13.8%); ST3,n= 9/29 (31.0%); ST19A,n= 12/29 (41.4%); ST7F/7A,n= 1/29 (3.4%); ST9V/9A,n= 1/29 (3.4%); ST22F/22A,n= 2/29 (6.9%). Over the same period, 361 IPD patients, aged 16 years or less, were notified to NNDSS. Among 331 serotypeable NNDSS isolates (71.5% from blood), the frequencies of ST1 and 3 were significantly lower than in PF samples: ST1,n= 8/331 (2.4%;P< 0.05); ST3,n= 13/331 (3.9%;P< 0.0001).The use of PCR to identify and serotype SP in culture-negative specimens provides additive information.