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• Frequency-dependent selection in vaccine-associated pneumococcal population dynamics  + (Many bacterial species are composed of mul … Many bacterial species are composed of multiple lineages distinguished by extensive variation in gene content. These often co-circulate in the same habitat, but the evolutionary and ecological processes that shape these complex populations are poorly understood. Addressing these questions is particularly important for Streptococcus pneumoniae, a nasopharyngeal commensal and respiratory pathogen, as the changes in population structure associated with the recent introduction of partial-coverage vaccines have significantly reduced pneumococcal disease. Here we show pneumococcal lineages from multiple populations each have a distinct combination of intermediate frequency genes. Functional analysis suggested these loci were likely subject to negative frequency-dependent selection (NFDS) through interactions with other bacteria, hosts, or mobile elements. Correspondingly, these genes had similar frequencies in four populations with dissimilar lineage compositions. These frequencies were maintained following substantial alterations in lineage prevalences once vaccination programmes began. Fitting a multilocus NFDS model of post-vaccine population dynamics to three genomic datasets using Approximate Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:ject always to the full Conditions of use:)

• Frequency-dependent selection in vaccine-associated pneumococcal population dynamics  +