Analysis of genomic diversity and evolution of the low-level antiseptic resistance gene smr in Staphylococcus aureus

A multidrug efflux pump specified by the smr gene mediates low-level antiseptic resistance in staphylococci. We analyzed the genomic diversity of smr and its gene cassette, a structural unit containing smr and terminal direct repeats (DRs), in 22 clinical strains of Staphylococcus aureus isolated over 9 years in a Japanese hospital. Although open reading frames (ORFs) of all the smr genes examined were identical to those reported previously (e.g., qacD in pSK41), smr gene cassettes were classified into three groups (types 1, 2, and 3). The type 1 cassette had an identical genetic organization to that found in the plasmid pSK41, a putative prototype of the smr gene cassette, which contains DRs flanking smr. In the type 2 cassette, the rep gene and a putative replication nick site were found upstream of smr, between a SSOA (single-strand origin) sequence and DR1(c), which are components of the type 1 cassette DR. In the type 3 cassette detected in a single strain, IS431 was located between the 3' end of smr and DR. It was suggested by genomic comparison that type 2 and type 3 cassettes might have been derived from the type I cassette via insertion of foreign DNA sequence, and that the type 2 cassette might be a precursor form of some previously reported smr cassettes, such as those in pSK108 and pNVH99. Although MICs of antiseptics and ethidium bromide were generally the same among strains having type 1, 2, or 3 smr gene cassette, the type 1 cassette was detected most frequently. Moreover, the copy number of the smr gene in the type 2 cassette was found to be much higher than that in the type 1 or type 3 cassette.