The structure of genetic diversity in a bacterial species

Staphylococcus aureus is a common human pathogen, and as a result is frequently sequenced. We take advantage of this by processing and analyzing >80,000 publicly available whole-genome shotgun sequences to characterize the diversity of this species in depth. We find that allelic diversity in the core genome partitions S. aureus into clear subspecies, with individuals within each subspecies >99.5% identical to each other at the nucleotide level. We find that the accessory genome also gives this same partitioning, but that this is due to a subset of accessory genes, with other genes shared across subspecies. We discuss possible evolutionary mechanisms that could have produced these patterns and future directions for investigating within-species bacterial diversity.