Convergent Evolution Driven by Rifampin Exacerbates the Global Burden of Drug-Resistant Staphylococcus aureus

Area of Science:

• Microbiology and Infectious Diseases
• Genomics and Molecular Biology
• Antimicrobial Resistance

Background:

• Mutations in the RNA polymerase beta-subunit (RpoB) confer rifampin resistance (Rif^r) in Staphylococcus aureus.
• Previous in vitro studies suggested RpoB mutations might decrease susceptibility to other antibiotics, but clinical relevance remained unclear.

Purpose of the Study:

• To investigate the clinical relevance and genomic impact of prevalent RpoB mutations in Staphylococcus aureus.
• To determine if common RpoB mutations contribute to cross-resistance to last-line antibiotics and therapeutic failure.

Main Methods:

• Analysis of 7,099 clinical S. aureus genomes to identify prevalent Rif^r-associated RpoB mutations.
• Recreation of specific RpoB mutations (H481N/Y and others) in S. aureus to assess phenotypic effects.
• Evaluation of susceptibility to vancomycin and daptomycin in mutated strains, including small-colony variants (SCVs).

Main Results:

• Eight RpoB mutations accounted for 93% of Rif^r mutations, with H481N/Y substitutions linked to global Rif^r clone expansion.
• H481N mutation did not affect growth but promoted stable Rif^r SCVs with reduced susceptibility to vancomycin and daptomycin.
• 86% of Rif^r isolates showed cross-resistance to vancomycin, and 52% to both vancomycin and daptomycin.

Conclusions:

• Prevalent RpoB mutations drive clinically relevant phenotypic plasticity, leading to stable, multidrug-resistant S. aureus lineages.
• These mutations increase the risk of therapeutic failure via SCV generation and cross-resistance to last-line agents.
• Recommendations include lowering rifampin susceptibility breakpoints and reconsidering its use to curb the spread of deleterious mutations.