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Pneumococcal conjugate vaccines have reduced the incidence of invasive pneumococcal disease,
caused by vaccine serotypes, but non-vaccine-serotypes remain a concern. We used whole genome sequencing
to study pneumococcal serotype, antibiotic resistance and invasiveness, in the context of genetic background.
Methods: Ourdatasetof 13,454genomes, combinedwithfourpublishedgenomicdatasets, representedAfrica (40%),
clustered into lineages using PopPUNK, and named Global Pneumococcal Sequence Clusters (GPSCs). From our
dataset,weadditionallyderivedserotypeandsequencetype,andpredictedantibiotic sensitivity.Wethenmeasured
invasiveness using odds ratios that relating prevalence in invasive pneumococcal disease to carriage.