Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory
genomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamics
of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), which
maintains accessory loci at equilibrium frequencies. Long-term simulations demonstrated NFDS stabilised clonally-evolving
multi-strain populations through preventing the loss of variation through drift, based on polymorphism frequencies,
pairwise genetic distances and phylogenies. However, allowing symmetrical recombination between isolates evolving under
multi-locus NFDS generated unstructured populations of diverse genotypes. Replication of the observed data improved
when multi-locus NFDS was combined with recombination that was instead asymmetrical, favouring deletion of accessory
loci over insertion. This combination separated populations into strains through outbreeding depression, resulting from
recombinants with reduced accessory genomes having lower fitness than their parental genotypes. Although simplistic
modelling of recombination likely limited these simulations’ ability to maintain some properties of genomic data as
accurately as those lacking recombination, the combination of asymmetrical recombination and multi-locus NFDS could
restore multi-strain population structures from randomised initial populations. As many bacteria inhibit insertions into their
chromosomes, this combination may commonly underlie the co-existence of strains within a niche.