Schematic representation of rRNA operons in S. aureus and PCR strategy. (A) Locations of the six rRNA operons on the genome of strain COL. (B) Organization of the rRNA operons. Operon 3 is lacking in strains with five operon copies. Two PCRs were performed: PCR-1 is indicated with light and dark gray arrows. In isolates with five copies of the rRNA operon in PCR-1, only a product of 2,363 bp (light gray arrows) will be amplified, whereas in isolates with six copies, both the 2,363-bp product and a 1,715-bp fragment (dark gray arrows) will be yielded (COL is an exception due to a smaller intergenic region between the 5S and 16S genes, where the amplification products will be of similar sizes; indicated by an asterisk). The black arrows indicate the products formed by the seminested PCR (PCR-2), consisting of a product of 1,534 bp when the third operon is present and a 16S internal control (216 bp). (C) Amplification products formed for strains with either six or five rRNA operon copies.