Nasopharyngeal colonization by Streptococcus pneumoniae and other common bacteria eight years following introduction of pneumococcal conjugate vaccine in rural South African children ≤5 years old.

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Streptococcus pneumoniae remains a leading cause of morbidity and mortality in children <5-years-old in sub-Saharan Africa. Monitoring serotype-specific nasopharyngeal colonisation can serve as a proxy to evaluate the effect of vaccination against vaccine-serotype (VT) disease. We evaluated the impact of 13-valent pneumococcal conjugate vaccine (PCV13, 2+1 schedule) immunisation on pneumococcus, and other bacterial colonisation among healthy rural South African children <60-months-old, eight years after PCV introduction. Nasopharyngeal swabs collected during two cross-sectional surveys in the Bushbuckridge sub-district, Mpumalanga from May-October 2009 (Period-1, 630) and July 2017-February 2018 (Period-2, 568) and tested for 92 pneumococcal serotypes and 15 other bacteria using high-throughput real-time PCR. Comparing Period-2 to Period-1, there was a lower overall (76.9% vs. 83.2%, adjusted Odds Ratio [aOR]:0.65, 95%CI:0.48-0.87) and PCV13-VT colonisation prevalence (14.3% vs. 51.0%; aOR:0.16, 95%CI:0.12-0.21). In Period-2 VT 19F (5.3%) and 6B (4.8%) dominated, albeit at a lower prevalence compared with Period-1 (10.3%, aOR:0.52, 95%CI:0.33-0.82 and 15.2%, aOR:0.26, 95%CI:0.16-0.41, respectively). Non-vaccine-serotype (NVT) colonisation was higher in Period-2 (63.2%) than Period-1 (35.6%, aOR:3.12, 95%CI:2.45-3.97), driven by 16F (8.1% vs. 0.3%) and 23B (5.1% vs. 3.5%). Non-typeable pneumococci were higher in Period-2 (21.8%) compared with Period-1 (12.5%, aOR:1.94, 95%CI:1.42-2.67). Other differences included a higher prevalence in Period-2 of Acinetobacter baumannii (36.8% vs 1.1%, aOR:50.11, 95%CI:23.14-108.50), Klebsiella pneumoniae (13.2% vs 0.6%, aOR:22.16, 95%CI:8.03-61.11), Streptococcus pyogenes (2.5% vs 0.2%, aOR:14.49, 95%CI:1.89-111.09) and Neisseria lactamica (8.1% vs 4%, aOR:2.14, 95%CI:1.28-3.57), whereas Streptococcus oralis (0.5% vs 2.2%, aOR:0.21, 95%CI:0.06-0.77) and Moraxella catarrhalis (60.4% vs 67.8%, aOR:0.72, 95%CI:0.56-0.91) were lower. There was an 80% lower prevalence of PCV13-VT serotype colonisation after eight years of routine PCV immunisation, however, there was high residual prevalence of 19F and 6B, serotypes that also persist in disease. The clinical relevance of temporal changes in colonization by other bacteria warrant further investigation.

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