Genome Plasticity of <i>agr</i> -Defective Staphylococcus aureus during Clinical Infection

Abstract

Therapy for bacteremia caused by <i>Staphylococcus aureus</i> is often ineffective, even when treatment conditions are optimal according to experimental protocols. Adapted subclones, such as those bearing mutations that attenuate <i>agr</i>-mediated virulence activation, are associated with persistent infection and patient mortality. To identify additional alterations in <i>agr</i>-defective mutants, we sequenced and assembled the complete genomes of clone pairs from colonizing and infected sites of several patients in whom <i>S. aureus</i> demonstrated a within-host loss of <i>agr</i> function. We report that events associated with <i>agr</i> inactivation result in <i>agr</i>-defective blood and nares strain pairs that are enriched in mutations compared to pairs from wild-type controls. The random distribution of mutations between colonizing and infecting strains from the same patient, and between strains from different patients, suggests that much of the genetic complexity of <i>agr</i>-defective strains results from prolonged infection or therapy-induced stress. However, in one of the <i>agr</i>-defective infecting strains, multiple genetic changes resulted in increased virulence in a murine model of bloodstream infection, bypassing the mutation of <i>agr</i> and raising the possibility that some changes were selected. Expression profiling correlated the elevated virulence of this <i>agr</i>-defective mutant to restored expression of the <i>agr</i>-regulated ESAT6-like type VII secretion system, a known virulence factor. Thus, additional mutations outside the <i>agr</i> locus can contribute to diversification and adaptation during infection by <i>S. aureus agr</i> mutants associated with poor patient outcomes.