Three Accessory Gene Clusters Drive Host-Adaptation in Group B Streptococcus

Streptococcus agalactiae (Group B Streptococcus, GBS) is a major pathogen of humans and animals, posing a threat to human health as well as food security. Here, we investigate the role of genomic mechanisms, including homologous recombination and horizontal gene transfer, in shaping the population structure of GBS and its adaptation to three major host groups (humans, cattle, fishes). We demonstrate that the GBS population comprises host-specialist, host-adapted lineages as well as host generalists, and that these categories differ in their level or recombination. Although the accessory genome at large varies by lineage rather than host, genome wide association studies show that host association is driven by three accessory genome clusters, regardless of lineage or breadth of the host spectrum. These genomic clusters (scpB in human GBS, lactose operon in bovine GBS, Locus 3 in fish GBS) are known (scpB, Lac.2) or shown here (Locus 3) to be functionally relevant and are shared with other streptococcal species occupying the same host niche. These findings demonstrate the importance of considering the role of non-human host species in the evolution of GBS, including high risk clones that may lead to interspecies transmission and affect efficacy of future GBS vaccines.