Multiplex PCR Assay for Detection of Pneumococcal Serotypes in Nasopharyngeal Samples of Healthy Children; Tehran, 2009-2010

Background: Streptococcus pneumoniae (S. pneumoniae), is a major pathogen causing invasive disease, colonizes the nasopharynx constituting a potential source of infection in both children and adults.
Aims: To identify the rate of pneumococcal nasopharyngeal colonization in healthy infants <2 years of age and to define the prevalent serotypes.
Materials and Methods: This cross-sectional study was performed for three months from June to August 2009 on healthy children, aged 6, 12 and 18 months visiting Health centers for routine vaccinations. Trained personnel collected nasopharyngeal samples through flexible nasal swabs and sent the specimens for diagnosis of pneumococci; after DNA extraction, microorganisms were serotyped by Multiplex PCR assay.
Results: One thousand two hundred ninety one samples were collected. S. pneumoniae was identified in 34%. A total of 761 identified S. pneumoniae, belonging to 30 different serotypes were recovered from 441 positive nasopharyngeal specimens. Serotypes 19, 6, 14, 19F, 17, 21, 20, 12F, 11 and three were most common, isolated in frequencies of 8.2, 7.6, 7.2, 7.2, 6.4, 5.3, 5.1, 4.8, 4.5 and 4.3% respectively. There was no significant difference in the diagnosed serotypes from the three age groups. Eleven serotypes (38.5%) are included in the 13-valent pneumococcal conjugate vaccine, (PCV 13). Colonization with more than one strain was seen in 228 samples, (52% of carriers).
Conclusion: Our findings revealed a significant rate of nasopharyngeal colonization with S. pneumoniae in young carriers; and draw attention to fact that only 38.5% of the isolated serotypes are included in PCV 13, demonstrating limited coverage of the current vaccine. There is a need to manufacture vaccines with an optimal formulation that would provide effective protection against serotypes prevalent in the community.