Streptococcus pneumoniae and other bacterial nasopharyngeal colonization seven years post-introduction of 13-valent pneumococcal conjugate vaccine in South African children

•Pneumococcal conjugate vaccines have modestly reduced circulating vaccine serotypes in Soweto, South Africa.•There is a residual of vaccine serotypes.•Colonization by vaccine-serotype 19F remains high.•Co-colonization is higher in our setting than observed elsewhere. Pneumococcal conjugate vaccines (PCVs) reduce pneumococcal-associated disease by reducing vaccine-serotype (VT) acquisition in vaccinated children, thereby interrupting VT transmission. The 7-valent-PCV was introduced in the South African immunization program in 2009 (13-valent-PCV since 2011) using a 2+1 schedule (at 6, 14, and 40 weeks of age). We aimed to evaluate temporal changes in VT and non-vaccine-serotype (NVT) colonization after 9 years of childhood PCV immunization in South Africa. Nasopharyngeal swabs were collected from healthy children