Identification of a novel mutation at the primary dimer interface of GyrA conferring fluoroquinolone resistance in Clostridium difficile

•First reported non-QRDR mutation conferring fluoroquinolone resistance in Clostridium difficile.•GyrA Ala384Asp has a pleiotropic effect on resistance: fluoroquinolones+novobiocin.•Extra-QRDR polymorphisms are present in fluoroquinolone-resistant isolates.•Strains devoid of gyrBA polymorphisms exhibit DNA gyrase-independent resistance.•In silico analysis revealed a diversity of extra-QRDR polymorphisms in DNA gyrase.