Whole-genome sequencing to elucidate possible mechanism of E. coli adaptation to antimicrobial therapy

Chemostat continuous culture systems were used to investigate adaptation of E. coli to a novel antimicrobial agent (ITC) and resistance to levofloxacin (LVX) under nutrient limiting environment. Three separate enrichment continuous cultures of E. coli ATCC 25922 were operated (D=0.4 h-1, 480 h) to select for ITC-adapted and LVX-resistant mutants, and compared with selection-free cultures. The derivative culture from the chemostat run under LVX-selection pressure showed resistance towards LVX (MIC of LVX increased 64-fold), and yet, no tolerance was observed towards ITC. Chemostats operated with ITC-selection pressure yielded population with no altered susceptibility towards ITC, as well as LVX. These results revealed that ITC usage is not promoting tolerance to itself, and no cross-resistance to antibiotics. The aim of this study is to use whole-genome sequence analysis to screen for mutagenesis, to reveal the repertoire of point mutations and to uncover the genetic basis of evolutionary adaptations.