In order to compare the groups of infection-associated (INF, n = 23) and commensal isolates (nCloNo, n = 62), a virtual INF isolate for each infection was calculated by averaging the values of phenotype variables of all INF isolates from one infection (2–10 INF isolate per patient -> compiled into one virtual isolate by averaging values of variables -> one virtual isolate per infection goes into comparison with nCloNo isolates, as not to introduce a bias into the comparison by adding more than one isolate per infection). Phenotypes were tested for a symmetric distribution and transformed to a logarithmic scale in order to attain normal distribution where appropriate. Metric variables were analysed by Student’s t-Test. Categorical variables were tested by Pearson’s chi-square. Statistical significance was accepted at a p-value ≤0.05. Analyses were conducted in SPSS version 25 (IBM, Armonk, NY, USA). Plots were created in R with the ggplot2 package[101] and GraphPad Prism v5 (GraphPad Software, La Jolla, CA, USA).

In order to compare phenotypes of INF isolates CloNo isolates, we used mixed models with the individual patient as random intercept. To analyse metric variables, a linear mixed model was used. Variables were log10-transformed where appropriate, in order to attain symmetrically distributed values and residues. Results are reported as either mean effect size between INF and CloNo isolates or in case of log-transformed variables, as a factor (10 to the power of co-efficient). P-value and 95% confidence interval of mean effect size or factor are given. Categorical variables were analysed in a mixed ordinal regression model. Results are reported as odds ratio (OR), 95% confidence interval of OR and p-value. Statistical significance was accepted at a p-value <0.05. Analyses were conducted in SPSS version 25 (IBM, Armonk, NY, USA).

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