Tables with Supplementary Information.
(A) Calculation of estimated generation times of infecting clone types. For each, the patient ID, clone type, length of infection in years and minutes, estimated doubling time and calculated number of generations is given. A doubling time of 74 min was used for clonal lineages infecting for less than 6 years, 83 min for 6–24 years and 109 min for >24 years based on the measurements of Yang et al. (2011). This is, to our knowledge, the best available for CF conditions. (B) Overview of patients and isolates. For each patient is given the ID, the number of samples, the year of first sample, the extent of sampling in years, whether pyoverdine non-producers were sampled, the number of clone types sampled, and the clone type name(s). (C) List of mutations in genes associated with iron metabolism. For each isolate, the patient ID, clone type and mutations are listed. A //denotes an intergenic mutation. The isolate names refer to previous descriptions (Andersen et al., 2015; Markussen et al., 2014; Marvig et al., 2015). The six DK1 isolates that were not included in the previous analysis of pyoverdine mutations had one ns SNP in pvdL (A5702G) and one in pvdP (C1508T, patient P55M3, isolate TM50 and TM51). The six isolates used in the phenotypic assay of phuS//phuR mutations are highlighted in yellow. (D) Summary of the mutations found in five different iron uptake systems in P. aeruginosa. The size of the respective systems is given in kb, and mutations are listed as non-synonymous (ns) SNPs, synonymous (syn) SNPs, insertions and deletions (indels) and intergenic (IG). The overall mutations, and ns SNPS and indels, per kb are listed. The phu operon experienced the highest mutation rate, dominated by intergenic mutations. Two genes in the has operon were poorly sequenced in the majority of isolates, and this is taken into account in the size and mutations listed in parentheses. (E) Mutations identified in pyoverdine over-producers that may contribute to this phenotype. For each mutation, the patient ID, clone type and gene is listed, as well as a reference to previous work showing a link between the gene and pyoverdine production (Frangipani et al., 2014; Ochsner et al., 2002; Stintzi et al., 1998; Visaggio et al., 2015; Wu et al., 2004). (F) Transitions between iron uptake systems characterized as the order in which mutations accumulate. When a clear order of mutations could be established the observed and expected number of transitions, given a Poisson distribution, is stated and whether the difference between them is statistically significant. (G) Results of Tukey HSD post hoc comparison of a Two-Way ANOVA analysing the difference in Max OD600 between an isogenic pair of isolates differing in a phuS//phuR mutation at four different heme concentrations.