Genotypic and phenotypic antimicrobial resistance of Clostridioides difficile in the Irish population, 2022
Objectives Infection with Clostridioides difficile (C. difficile) usually occurs after antibiotic treatment for other infections and can cause gastro-intestinal disorders of variable severity. C. difficile can be resistant to a wide spectrum of antimicrobials. Detection of antimicrobial resistance (AMR) is important to direct optimal treatment and surveillance of AMR patterns in the overall population. Correlation between genotypic markers and phenotypic AMR is not yet well defined. The aim for this study is to assess whether phenotypic resistance can be predicted from genetic markers. Methods 99 C. difficile isolates were phenotypically characterized for resistance to eight antibiotics using ANAERO3 sensititre plates and E-tests. Their genomes were screened for genetic markers of resistance. Accuracy, sensitivity, specificity, positive and negative predictive values were calculated for each antibiotic. Results We found high rates of resistance (>50%) to cefoxitin and clindamycin, intermediate rates of resistance (10% - 50%) to moxifloxacin and tetracycline and low rates of resistance (<10%) to imipenem, metronidazole, vancomycin and rifampicin. For moxifloxacin, tetracycline and clindamycin, we found a good correlation between genotypic and phenotypic AMR, with an overall accuracy of 94% (95% CI 87%-98%), 78% (95% CI 68%-86%) and 86% (95% CI 77%-92%) respectively. For the other five antibiotics, accurate estimates on the correlation could not be made.  Conclusion Our results suggest that for moxifloxacin, tetracycline and clindamycin, phenotypic resistance in C. difficile can be predicted by genetic indicators and used for public health purposes. However, for the other five antibiotics, the model is not accurate and further development is necessary.