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An observational study was performed to investigate the carriage rate and serotypes of Streptococcus pneumoniae in the 13-valent pneumococcal conjugate vaccine (PCV13) era in Taiwan.From March 2014 to March 2015 a total of 500 healthy children and their households (631 adults) were enrolled from two large medical centres for nasopharyngeal carriage survey. Clinical isolates were prospectively collected from June 2012 to May 2015 at Chang Gung Memorial Hospital. We applied a multiplex polymerase chain reaction in addition to culture to detect S. pneumoniae.S. pneumoniae was isolated from 12.0% of the children and 3.6% of the households. In the children's cohort only 23.3% of the isolates could be assigned to PCV13 serotypes; non-vaccine serotypes were predominant (76.6%) and the most frequently detected non-vaccine serotypes were 15A/F and 15B/C (both 13.3%), followed by 23A (6.7%). In the household cohort, 21.7% belonged to PCV13 serotypes, and 78.3% to non-vaccine serotypes. Clinical analysis of culture-confirmed pneumococcal infection showed that infection caused by PCV13 serotypes decreased by 47% from 83% in 2012-2013 to 44% in 2014-2015, while infection caused by non-PCV13 serotypes increased from 17 to 56%. Among the carriage isolates a significantly higher percentage belonged to serogroup 15 compared to serogroup 19 (26.6 vs 6.66%, 2014-2015; P=0.003). Therefore, clinical isolates belonging to serogroup 15 were more prevalent than those belonging to serogroup 19 (44.1 vs 32.3%, 2014-2015; P=0.318).The isolation of non-vaccine serotypes and unknown serotypes after the introduction of PCV13 in children highlights the importance of continued surveillance for emerging serotypes.