Quantifying the determinants of evolutionary dynamics leading to drug resistance

Resistance evolution experiments in nitrofurantoin and chloramphenicol were carried out in the morbidostat as described [1]. Six replicate experiments were performed for each drug; all experiments were run in parallel. The IC50 of evolved populations (Fig. 4C,D) was measured as described [1]. One clone was isolated from each of the six replicates and whole genome sequencing was performed for these clones and the MG1655 ancestor. Genomic DNA was purified from overnight cultures using the Promega Wizard Genomic DNA Purification Kit (catalogue number A1120). Library preparation, multiplexing, and sequencing were performed at the EMBL GeneCore facility. The samples were sequenced on an Illumina HiSeq2000 (paired-end sequencing, 100bp read length, ~140-fold coverage). [1]Toprak E, Veres A, Michel J-B, Chait R, Hartl DL, Kishony R. Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat Genet. 2012;44: 101–5. doi:10.1038/ng.1034