Dynamics of Colonization and Recolonization of Streptococcus pneumoniae Strains in Healthy Peruvian Children

Background: Streptococcus pneumoniae (Spn) colonizes the nasopharynx of healthy children and contributes to global child mortality. Though introduction of pneumococcal vaccines has certainly decreased carriage of vaccine types, there is less known about effects on complex carriage dynamics, including the order and frequency of Spn colonization by serotype. Methods: We assessed Spn carriage dynamics in Peru, where the 7-valent pneumococcal vaccine (PCV7) was introduced in late 2009. Nasopharyngeal (NP) samples were collected monthly from healthy children less than 3 years of age in 2009 and 2011. Spn was isolated from NP samples by culture and Quellung serotyped. DNA was extracted from NP samples to analyze bacterial density using lytA-based qPCR. Results: The proportion of children with at least one detection of Spn was similar in children before (2009) and after (2011) PCV7 introduction: 92% (471/510) and 89% (451/509), respectively. Among children with Spn detected at two or more visits, approximately half (56% and 45% in 2009 and 2011, respectively) had a different serotype detected at their last visit from the serotype detected at their first visit, with an average time between first and last visit of 86 days in 2009 and 76 days in 2011. Carriage of PCV7 serotypes was higher in 2009 than in 2011: 43% of first carriage events and 38% of last carriage events were vaccine serotypes in 2009, compared to 25% and 22% in 2011.  In 2009, serotypes 6A, 6B, and 6C were the most frequent ‘recolonizers’ (detected at last carriage but not at first carriage), whereas 11A/D and 23F were the most common ‘persisters’ (detected at both first and last carriage). In 2011, 15C, 19A and 23B were the most common recolonizers and 6B, 10A, and 11A, were the most common persisters. In 2011, NP density of recolonizers 15C and 19A was significantly higher when compared to other serotypes. In 2009, carriage of non-vaccine types increased from September to November; in 2011, non-vaccine types predominated in all months. Conclusion: Nearly all children in 2009 and 2011 (>89%) carried Spn. Notably, half of these children were recolonized by a different serotype, with strains of serogroup 6 most likely to recolonize children in 2009 and serotypes 19A, 23B, and 15C most likely to recolonize children in 2011.