Background: The distribution of serotypes causing invasive pneumococcal diseases are diverse, limiting the proportion of IPD cases pneumococcal conjugate vaccine can prevent. More studies are need to estimate the rate of pneumococcal acquisition and serotype replacement following introduction of pneumococcal conjugate vaccine.
Methods:The study was conducted in the department of microbiology of a tertiary hospital. Nasopharyngeal swabs were collected among 200 under five children from Pediatric outpatient department. Streptococcus pneumoniae  were isolated and identified by culture, Gram staining, biochemical test and polymerase chain reaction (PCR). An initial screening of the nasopharyngeal swabs were done by the primer cpsA to identify the pneumococci by monoplex PCR. Then primers that are serotype specific were used for serotyping by multiplex PCR with positive and negative control.
Results: Out of 200 nasopharyngeal swabs, 67 (33.50%) were positive by culture and 92 (46%) were positive by PCR for S. pneumoniae. Out of 200 children, 90 (45%) were received PCV and 110 (55%) were not vaccinated. Among vaccinated children, 3 (12%) S. pneumoniae were detected in fully vaccinated children and 19 (29.23%) S. pneumoniae were detected in partially vaccinated children by culture. In case of PCR, 4 (16%) S. pneumoniae were detected in fully vaccinated children and 25 (38.46%) S. pneumoniae were detected in partially vaccinated children. Among not vaccinated children, 45 (40.90%) and 63 (57.27%) S. pneumoniae were detected by culture and PCR respectively .The predominant serotypes were 34F, 35B, 6A, 6B, 14, 23F, 3, 19A, 19F, 4, 18C, 7F as carriage strains.
Conclusion. Children represent a consistent population of pneumococcal-naïve individuals. So, we found detection rate of S. pneumoniae and serotypes inchildren as carrier was relatively more in non-vaccinated children.