Severe infections emerge from commensal bacteria by adaptive evolution
2018
Bacteria responsible for the greatest global mortality colonize the human microbiota far more frequently than they cause severe infections. Whether mutation and selection among
commensalbacteria are associated with infection is unknown. We investigated
de novo mutationin 1163 Staphylococcus aureus genomes from 105 infected patients with
nosecolonization. We report that 72% of infections emerged from the
nose, with infecting and
nose-colonizing bacteria showing parallel adaptive differences. We found 2.8-to-3.6-fold adaptive enrichments of protein-altering variants in genes responding to rsp, which regulates surface antigens and toxin production; agr, which regulates
quorum-sensing, toxin production and abscess formation; and host-derived
antimicrobial peptides.
Adaptive mutationsin pathogenesis-associated genes were 3.1-fold enriched in infecting but not
nose-colonizing bacteria. None of these signatures were observed in healthy carriers nor at the species-level, suggesting infection-associated, short-term, within-host selection pressures. Our results show that signatures of spontaneous adaptive evolution are specifically associated with infection, raising new possibilities for diagnosis and treatment.
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