Fig. 4: Tandem amplification of sdrD::tetK.

a USA300 sdrD::tetK was grown over three consecutive days in six parallel cultures in the presence or absence of ciprofloxacin (CIP). Each day, the copy number of up to 16 clones of each culture showing high Tc resistance was screened by qPCR. Upper and lower box limits and the horizontal lines within the boxes represent 25 and 75% percentiles and the medians, respectively. The whiskers of the plots indicate minimum and maximum range. Data are derived from six independent experiments and represent: Day 1, n = 87 and n = 76 of “no Cip” and “1 µg/ml Cip”, respectively; Day 2, n = 90 and n = 95 of “no Cip” and “1 µg/ml Cip”, respectively; Day 3, n = 78 and n = 96 of “no Cip” and “1 µg/ml Cip”, respectively. All data points are shown. Datasets were not normal distributed (D’Agostino & Pearson omnibus test <0.0001) and statistical analysis was performed using two-tailed Mann–Whitney test. Source data are provided as a Source Data file. b Frequency of amplification (Tc₂₀-resistant clones showing at least a 2 fold increase in csa1 copy number compared to the parental strain by qPCR) within the total population of living cells. Shown are the results of six independent experiments. x indicates a culture in which amplification was not detected. Source data are provided as a Source Data file. c sdrD copy number of a high Tc-resistant strain in comparison to the parental strain measured by qPCR. Mean and SD of three replicate qPCRs on a single DNA isolation is shown. Source data are provided as a Source Data file. d MinION sequence analysis of the high Tc-resistant isolate. Single reads covering the sdrCDE array were aligned against the sdrD::tetK locus of the parental strain. Tandem amplifications manifest as multiple regions within the read with homology to sdrD::tetK. Connecting lines within the read are omitted for reasons of clarity. Genes sdrC, tetK, sdrD and sdrE are indicated. Source data are provided as a Source Data file.