Abstract
The emergence of new pathogens is a major threat to public and veterinary health. Changes in bacterial habitat such as a switch in host or disease tropism are typically accompanied by genetic diversification. Staphylococcus aureus is a multi-host bacterial species associated with human and livestock infections. A microaerophilic subspecies, Staphylococcus aureus subsp. anaerobius, is responsible for Morel’s disease, a lymphadenitis restricted to sheep and goats. However, the evolutionary history of S. aureus subsp. anaerobius and its relatedness to S. aureus are unknown. Population genomic analyses of clinical S. aureus subsp. anaerobius isolates revealed a highly conserved clone that descended from a S. aureus progenitor about 1000 years ago before differentiating into distinct lineages that contain African and European isolates. S. aureus subsp. anaerobius has undergone limited clonal expansion, with a restricted population size, and an evolutionary rate 10-fold slower than S. aureus. The transition to its current restricted ecological niche involved acquisition of a pathogenicity island encoding a ruminant host-specific effector of abscess formation, large chromosomal re-arrangements, and the accumulation of at least 205 pseudogenes, resulting in a highly fastidious metabolism. Importantly, expansion of ~87 insertion sequences (IS) located largely in intergenic regions provided distinct mechanisms for the control of expression of flanking genes, including a novel mechanism associated with IS-mediated anti-anti-sense decoupling of ancestral gene repression. Our findings reveal the remarkable evolutionary trajectory of a host-restricted bacterial pathogen that resulted from extensive remodelling of the S. aureus genome through an array of diverse mechanisms in parallel.
Highlights
Bacteria have a remarkable capacity to adapt to new environmental niches, a characteristic that underpins their potential to become successful pathogens
We discovered that S. aureus subsp. anaerobius evolved from an S. aureus ancestor and underwent an array of extensive changes to its genome that accompanied the transition to its current restricted lifestyle
We observed genome decay involving loss of function of hundreds of genes, large intra-chromosomal rearrangements affecting most of the genome, acquisition of a pathogenicity island, and expansion of large numbers of insertion sequences that are inserted at intergenic sites around the genome
Summary
Bacteria have a remarkable capacity to adapt to new environmental niches, a characteristic that underpins their potential to become successful pathogens. The evolutionary process of host restriction, observed across distantly-related bacterial groups, typically involves genomic events such as gene loss, gene acquisition, or chromosomal rearrangements [2,3,4,5]. The impact of such events may be most apparent after long-term associations between bacterium and host, with obligate intracellular pathogens the most extreme examples, exhibiting extremely small and compact genomes [6]. S. aureus has undergone extensive host-switching events during its evolutionary history leading to the emergence of new endemic and epidemic clones in livestock and humans [8]. A combination of gene acquisition, loss of gene function, and allelic diversification have been central to the capacity of S. aureus to undergo successful hostadaptation [8]
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