Fig. 1: csa1 gene copy number variation within the csa1 locus of S. aureus USA300 isolates.

a Schematic diagram of the three categories of repetitive sequences creating copy number variation. Hatched areas denote regions of homology. b Schematic representation of the deletions and putative amplifications of csa1 in different isolates. Coding sequences are indicated. Red and gray lines represent increased coverage (>2 fold) or deletions within the USFL isolates, respectively. c The upper panel shows the csa1 copy number of the indicated clinical isolates as measured by qPCR. Mean and SD of four replicate qPCRs on a single DNA isolation is shown. The lower panel shows DNA fragments amplified by conventional PCR using primers csa1_Sc.F and csa1_Sc.R indicated in (b). The experiment was performed once using the same batch of DNA used for qPCR. Source data are provided as a Source Data file. d USFL isolates were sequenced using MinION technology. For each sequenced isolate, a single long read that is aligned against the csa1 locus of USA300 FPR3757 is shown. Tandem amplifications manifest as multiple regions within the read with homology to csa1, allowing calculation of gene copy number. Hatched red lines emphasize that a single long read mapping repeatedly to the csa1 genes is analyzed. Genes csa1A, csa1B, csa1C, and csa1D are indicated. Shown are read_ch:51530_110 (USFL037); read_ch:10493_161 (USFL091); read_ch:40122_41 (USFL165). Source data are provided as a Source Data file.