Comparison of Phenotypic and Genotypic Antimicrobial Resistances in Bovine Clostridioides difficile Isolates

Background/Objectives: Antimicrobial agents play an important role in the pathogenesis and treatment of Clostridioides (C.) difficile infections. C. difficile isolates have shown different genotypic and phenotypic resistance patterns and could serve as antimicrobial resistance reservoirs. Methods: To gain insight into accordance and potential disagreements between genotypic and phenotypic antimicrobial resistances in C. difficile, we compared the genotypic and phenotypic resistance patterns of 108 bovine C. difficile isolates collected in Germany between 2010 and 2012. These isolates represent a collection of different ribotypes (RT) and originated from different husbandries in Germany. Whole genome sequencing of all isolates was performed with Illumina^® Miseq™, and sequences were screened for antimicrobial resistance determinants. For phenotypic antimicrobial susceptibility testing, the agar dilution procedure according to the CLSI document M11 was used. Minimal inhibitory concentration values were determined for penicillin, meropenem, tetracycline, moxifloxacin, vancomycin, metronidazole, erythromycin and clindamycin. Results: Various phenotypic and genotypic antimicrobial resistances were found in the isolates examined that belonged to different ribotype/sequence type (ST) lineages, even if these originated from the same source and geographical region (bovine isolates from Germany). Agreement between phenotypic and genotypic resistance was seen for most antimicrobial agents tested. A total of 92% (83/90) of the investigated ST11 isolates showed phenotypic resistance or were classified as non-wild type to at least one of the antimicrobials tetracycline, moxifloxacin, erythromycin and clindamycin. Conclusions: The results of this comparison contribute to a better understanding of antimicrobial resistance in C. difficile by relating phenotypic susceptibility patterns to genomic resistance determinants.