Repeated Emergence of Variant TetR Family Regulator, FarR, and Increased Resistance to Antimicrobial Unsaturated Fatty Acid among Clonal Complex 5 Methicillin-Resistant Staphylococcus aureus

Resistance-nodulation-division (RND) superfamily efflux pumps promote antibiotic resistance in Gram-negative pathogens, but their role in Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) is undocumented. However, recent selections for resistance of S. aureus to an antimicrobial fatty acid, linoleic acid, and an antibiotic, rhodomyrtone, identified H121Y and C116R substitution variants, respectively, in a TetR family regulator, FarR, promoting increased expression of the RND pump FarE. Hypothesizing that selection pressures have also promoted the emergence of FarR variants, we searched available genome data and found that strains with FarR from human and bovine hosts have emerged sporadically in clonal complexes (CCs) CC1, CC30, CC8, CC22, and CC97, whereas multiple FarR variants have occurred within CC5 hospital-associated (HA)-MRSA. Of these, FarR and FarR were exclusive to CC5, while FarR , FarR , and FarR also occurred in nonrelated CCs, primarily from bovine hosts. Within CC5, FarR and FarR strains were polyphyletic, each exhibiting two emergence events. FarR and FarR were individually sufficient to confer increased expression of FarE and enhanced resistance to linoleic acid (LA). Isolates with FarR were most closely related to S. aureus N315 MRSA and exhibited increased resistance independently of FarR . Accumulation of pseudogenes and additional polymorphisms in FarR strains contributed to a multiresistance phenotype which included fosfomycin and fusidic acid resistance in addition to increased linoleic acid resistance. These findings underscore the remarkable adaptive capacity of CC5 MRSA, which includes the polyphyletic USA100 lineage of HA-MRSA that is endemic in the Western hemisphere and known for the acquisition of multiple resistance phenotypes.