Whole-genome sequencing of a Clostridium difficile phenotypic mutant of increased fluoroquinolone resistance and its isogenic parent

The mechanisms of fluoroquinolone resistance in Clostridium difficile remain to be fully elucidated. We generated a phenotypic mutant of increased fluoroquinolone resistance under in vitro selection in the presence of the fluoroquinolone antibiotic ciprofloxacin. Targeted gene sequencing revealed the absence of conventional mutations in DNA gyrase which usually account for resistance in this species. To elucidate the mechanism of resistance in our phenotypic mutant, both mutant and isogenic parent were subjected to whole-genome sequence analysis.