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The workflow for analyses of the RNA-seq data is given in supplementary figure S2, Supplementary Material online.

Information about raw data is given in Supplementary Table 4. BNG maps were ordered and oriented on the basis of the POPSEQ genetic map.

A detailed description of the analysis strategy for the microarray data is given in Supplementary Materials S1.

Published polymorphisms were gathered from Mitomap and a table of the known polymorphisms found among the patient data is given in Supplementary Table 1.

Likewise, the statistical evolutionary trajectory index with statistical significance for zebrafish data is given in Supplementary Table 2, where we filtered out genes by coefficient of variation (CV) criteria remaining 12,034 genes.

A detailed description of the test data is given in the Supplementary Material.

The detailed methodological, mathematical and feature-based information, along with produced results (using GC-MS preprocessed experimental data), is given in the Supplementary Material.

The water mass of retentate and permeate, and lumen outlet pressure were recorded at 1 min intervals for 6 min; the raw data is given in the Supplementary Material Section 2. Based on this raw data, values of Q l,out and Qe,out are calculated by dividing the mass values (kg) by the product of the time interval (60 s) and water density (998.21 kg m−3 at 20°C).

We used a training set (St_A1) of 495 and a validation set (St_B1) of 471 S. aureus isolates that had been sequenced and phenotyped after being collected in Oxfordshire, UK (samples and phenotyping described in Methods section, Supplementary Fig. 1; accession codes and phenotyping data are given in Supplementary Data 1 and 3).

Sources of downloaded data are given in supplementary table S1 (Supplementary Material online).

Data are given in Supplementary Methods.