Colonization dynamics of Streptococcus pneumoniae in a remote African population: A prospective cohort study

•Gabonese pygmies were screened for nasopharyngeal S. pneumoniae colonization in 2011, 2013 and 2017.•Isolates were resistant to tetracycline (36–58%), penicillin (6–39%) and chloramphenicol (3–15%).•The distribution of serotypes was dynamic and very unstable throughout the six years.•The serotype coverage was low for PCV13 (37.3%) and PPSV23 (47.6%). The aim of this study was to analyze the population dynamics of Streptococcus pneumoniae in a remotely living African Pygmy population. The same pygmy population (Gabon) was prospectively screened for nasopharyngeal S. pneumoniae colonization in 2011 (n = 103), 2013 (n = 104) and 2017 (n = 107). Non-duplicate isolates (n = 126) were serotyped and tested for antimicrobial resistance (broth microdilution). At the three sampling time points, resistance rates were highest for tetracycline (36–58%), followed by penicillin (parenteral, meningitis-breakpoints, 6–39%) and chloramphenicol (3–15%). The majority of isolates was non-typeable (NT, n = 18/126, 14.3%) followed by serotype 6B (n = 17/126, 13.5%), 21 and 15A (n = 9/126, 7.1%, each). The distribution of serotypes was highly dynamic as only three serotypes (14, 17F, NT) were detected during all three visits. Resistance rates and serotypes of nasopharyngeal S. pneumoniae markedly changed in the remote Babongo population. This rapid change in serotypes could challenge the selection of pneumococcal vaccine.