Epistasis mediated alleviation of the cost of antibiotic resistance for MRSA

Understanding how multi-drug resistant pathogens evolve is key to identifying means of curtailing their further emergence. Theoretically, antibiotic resistance incurs a fitness cost to bacteria, however, the scale of this have been found to vary widely, with some resistance mechanisms reported to have little or no cost. One such apparently cost-free resistance mechanism acquired by the major human pathogen Staphylococcus aureus is to the clinically important antibiotic mupirocin, which is mediated by mutation of the isoleucyl-tRNA synthethase gene. In a recent GWAS study we reported that this mutation is associated with changes in the virulence of the bacteria, with the data suggesting this is driven through epistatic interactions with other loci. Here we report that in a subsequent geographically distinct collection of MRSA of the USA300 lineage we have found the same epistatic signal. We demonstrate that this resistance mutation reduces the expression of S. aureus toxins, which alleviates the costs associated with mupirocin resistance and explains the apparent lack of effect on fitness reported previously. Given the potential effect the mutation could have on enzyme activity and the subsequent translation of proteins containing high levels of isoleucine, we quantified the prevalence of isoleucine across all coding regions of the S. aureus genome. This identified key proteins of the toxin regulating Agr quorum sensing system, as well as four of the PSM family of toxins as having above average isoleucine content. For one of these proteins, AgrC, we found that shortly after induction there is a two-fold difference in the ability of the mupirocin resistant strain to translate the protein. We also found there to be significantly more free isoleucine in the cytoplasm of the mutant, suggesting it is not being incorporated into proteins at the same rate as the wild type strain. Although the effect of the mutation on AgrC translation was only temporary, we believe this delay in activation may have an effect on toxin expression, which in combination with the reduction in the expression of the PSMs may explain the effect on toxicity in the mupirocin resistant strain. This concomitant compensation of antibiotic resistance by offsetting the energetically-costly production of toxins through epistasis may help explain the rapid and successful emergence of this problematic antibiotic resistant pathogen.